scholarly journals Conformation-dependent restraints for polynucleotides: the sugar moiety

2019 ◽  
Vol 48 (2) ◽  
pp. 962-973
Author(s):  
Marcin Kowiel ◽  
Dariusz Brzezinski ◽  
Miroslaw Gilski ◽  
Mariusz Jaskolski
Keyword(s):  
Nucleic Acids ◽  
Crystal Structures ◽  
Protein Data Bank ◽  
Data Bank ◽  
Experimental Methods ◽  
Side Chain ◽  
Torsion Angles ◽  
Sugar Moiety ◽  
Structural Database ◽  
Different Parts

Abstract Stereochemical restraints are commonly used to aid the refinement of macromolecular structures obtained by experimental methods at lower resolution. The standard restraint library for nucleic acids has not been updated for over two decades and needs revision. In this paper, geometrical restraints for nucleic acids sugars are derived using information from high-resolution crystal structures in the Cambridge Structural Database. In contrast to the existing restraints, this work shows that different parts of the sugar moiety form groups of covalent geometry dependent on various chemical and conformational factors, such as the type of ribose or the attached nucleobase, and ring puckering or rotamers of the glycosidic (χ) or side-chain (γ) torsion angles. Moreover, the geometry of the glycosidic link and the endocyclic ribose bond angles are functionally dependent on χ and sugar pucker amplitude (τm), respectively. The proposed restraints have been positively validated against data from the Nucleic Acid Database, compared with an ultrahigh-resolution Z-DNA structure in the Protein Data Bank, and tested by re-refining hundreds of crystal structures in the Protein Data Bank. The conformation-dependent sugar restraints presented in this work are publicly available in REFMAC, PHENIX and SHELXL format through a dedicated RestraintLib web server with an API function.

scholarly journals Iron–sulfur clusters have no right angles

2019 ◽  
Vol 75 (1) ◽  
pp. 16-20 ◽  
Author(s):  
Nigel W. Moriarty ◽  
Paul D. Adams
Keyword(s):  
High Resolution ◽  
Protein Data Bank ◽  
Structure Refinement ◽  
Data Bank ◽  
Side Chain ◽  
Crystallographic Structure ◽  
Computational Tools ◽  
Iron Sulfur Clusters ◽  
Iron Sulfur ◽  
Structural Database

Accurate geometric restraints are vital in the automation of macromolecular crystallographic structure refinement. A set of restraints for the Fe4S4 cubane-type cluster was created using the Cambridge Structural Database (CSD) and high-resolution structures from the Protein Data Bank. Geometries from each source were compared and pairs of refinements were performed to validate these new restraints. In addition to the restraints internal to the cluster, the CSD was mined to generate bond and angle restraints to be applied to the most common linking motif for Fe4S4: coordination of the four Fe atoms to the side-chain sulfurs of four cysteine residues. Furthermore, computational tools were developed to assist researchers when refining Fe4S4-containing proteins.

Lithium-Protein Interactions: Analysis of Lithium-Containing Protein Crystal Structures Deposited in the Protein Data Bank

2020 ◽  
Vol 27 (8) ◽  
pp. 763-769
Author(s):  
Oliviero Carugo
Keyword(s):  
Small Molecules ◽  
Crystal Structures ◽  
Protein Data Bank ◽  
Protein Interactions ◽  
Structural Information ◽  
Protein Complexes ◽  
Aerospace Industry ◽  
Data Bank ◽  
Protein Crystal ◽  
Side Chain

Background: Despite the fact that lithium is not a biologically essential metallic element, its pharmacological properties are well known and human exposure to lithium is increasingly possible because of its used in aerospace industry and in batteries. Objective: Lithium-protein interactions are therefore interesting and the surveys of the structures of lithium-protein complexes is described in this paper. Methods: A high quality non-redundant set of lithium containing protein crystal structures was extracted from the Protein Data Bank and the stereochemistry of the lithium first coordination sphere was examined in detail. Results: Four main observations were reported: (i) lithium interacts preferably with oxygen atoms; (ii) preferably with side-chain atoms; (iii) preferably with Asp or Glu carboxylates; (iv) the coordination number tends to be four with stereochemical parameters similar to those observed in small molecules containing lithium. Conclusion: Although structural information on lithium-protein, available from the Protein Data Bank, is relatively scarce, these trends appears to be so clear that one may suppose that they will be confirmed by further data that will join the Protein Data Bank in the future.

scholarly journals Validation and correction of Zn–Cys x His y complexes

2016 ◽  
Vol 72 (10) ◽  
pp. 1110-1118 ◽  
Author(s):  
Wouter G. Touw ◽  
Bart van Beusekom ◽  
Jochem M. G. Evers ◽  
Gert Vriend ◽  
Robbie P. Joosten
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Model Validation ◽  
Data Bank ◽  
Zinc Complexes ◽  
Zinc Ions ◽  
Tetrahedral Complex ◽  
Context Sensitive

Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn–Cys distances and Cys–Zn–Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.

scholarly journals IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank

2013 ◽  
Vol 41 (W1) ◽  
pp. W432-W440 ◽  
Author(s):  
Nurul Nadzirin ◽  
Peter Willett ◽  
Peter J. Artymiuk ◽  
Mohd Firdaus-Raih
Keyword(s):  
Amino Acid ◽  
Protein Data Bank ◽  
Data Bank ◽  
Side Chain ◽  
Amino Acid Side Chain

Use of Patterson-based methods automatically to determine the structures of heavy-atom-containing proteins with up to 6000 non-hydrogen atoms in the asymmetric unit

2006 ◽  
Vol 39 (5) ◽  
pp. 728-734 ◽  
Author(s):  
Maria Cristina Burla ◽  
Rocco Caliandro ◽  
Benedetta Carrozzini ◽  
Giovanni Luca Cascarano ◽  
Liberato De Caro ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Protein Data Bank ◽  
Heavy Atom ◽  
Data Bank ◽  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Hydrogen Atoms ◽  
Heavy Atoms ◽  
Density Maps ◽  
Resolution Data

The Patterson superposition methods described by Burlaet al.[J. Appl. Cryst.(2006),39, 527–535], based on the use of the `multiple implication functions', have been enriched by supplementary filtering techniques based on some general (resolution-dependent) features of both the Patterson and the electron density maps. The method has been implemented in a modified version of the programSIR2004and tested using a set of 20 crystal structures selected from the Protein Data Bank, having a number of non-hydrogen atoms in the asymmetric unit larger than 2000, atomic resolution data and some heavy atoms (equal to or heavier than Ca). The new phasing procedure is able to solve most of the test structures, among which there are two proteins with more than 6000 non-hydrogen atoms in the asymmetric unit, so extending by far the complexity today commonly considered as the limit for Patterson-based methods (i.e.about 2000 non-hydrogen atoms).

scholarly journals Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules

1998 ◽  
Vol 54 (6) ◽  
pp. 1078-1084 ◽  
Author(s):  
Joel L. Sussman ◽  
Dawei Lin ◽  
Jiansheng Jiang ◽  
Nancy O. Manning ◽  
Jaime Prilusky ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Protein Data Bank ◽  
Structural Information ◽  
National Laboratory ◽  
Three Dimensional ◽  
Data Bank ◽  
Brookhaven National Laboratory ◽  
Biological Macromolecules

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submittedviaPDB's WWW-based toolAutoDep, in either mmCIF or PDB format, and are most conveniently examinedviaPDB's WWW-based tool3DB Browser.

ACMS: a database of alternate conformations found in the atoms of main and side chains of protein structures

2019 ◽  
Vol 52 (4) ◽  
pp. 910-913 ◽  
Author(s):  
R. Santhosh ◽  
P. Chandrasekaran ◽  
Daliah Michael ◽  
K. Rangachari ◽  
Namrata Bankoti ◽  
...  
Keyword(s):  
High Resolution ◽  
Knowledge Base ◽  
Crystal Structures ◽  
Protein Structures ◽  
Protein Molecule ◽  
Data Bank ◽  
Side Chain ◽  
Biological Macromolecules ◽  
Conformational Ensembles ◽  
User Friendly

Proteins are usually dynamic biological macromolecules, thereby exhibiting a large number of conformational ensembles which influence the association with their neighbours and interacting partners. Most of the side-chain atoms and a few main-chain atoms of the high-resolution crystal structures deposited in the Protein Data Bank adopt alternate conformations. This kind of conformational behaviour prompted the authors to explore the relationship, if any, between the alternate conformations and the function of the protein molecule. Thus, a knowledge base of the alternate conformations of the main- and side-chain atoms of protein structures has been developed. It provides a detailed description of the alternate conformations of various residues for more than 60 000 high-resolution crystal structures. The proposed knowledge base is very user friendly and has various flexible options. The knowledge base will be updated periodically and can be accessed at http://iris.physics.iisc.ac.in/acms.

Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

2020 ◽  
Vol 76 (5) ◽  
pp. 428-437 ◽  
Author(s):  
Wan-Ting Jin ◽  
Min Yang ◽  
Shuang-Shuang Zhu ◽  
Zhao-Hui Zhou
Keyword(s):  
Error Analysis ◽  
Crystal Structures ◽  
Protein Data Bank ◽  
Data Bank ◽  
Bond Valence ◽  
Crystallographic Data ◽  
Data Sets ◽  
Electron Configuration ◽  
The Individual ◽  
Bond Valence Method

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

scholarly journals π–π Noncovalent Interaction Involving 1,2,4- and 1,3,4-Oxadiazole Systems: The Combined Experimental, Theoretical, and Database Study

Molecules ◽  
2021 ◽  
Vol 26 (18) ◽  
pp. 5672
Author(s):  
Sergey V. Baykov ◽  
Alexander S. Mikherdov ◽  
Alexander S. Novikov ◽  
Kirill K. Geyl ◽  
Marina V. Tarasenko ◽  
...  
Keyword(s):  
Crystal Structures ◽  
13C Nmr Spectroscopy ◽  
Data Bank ◽  
Noncovalent Interaction ◽  
X Ray Diffraction ◽  
1H And 13C Nmr ◽  
Nci Analysis ◽  
Equilibrium Structures ◽  
Structural Database ◽  
Anti Hiv

A series of N-pyridyl ureas bearing 1,2,4- (1a, 2a, and 3a) and 1,3,4-oxadiazole moiety (1b, 2b, 3b) was prepared and characterized by HRMS, 1H and 13C NMR spectroscopy, as well as X-ray diffraction. The inspection of the crystal structures of (1–3)a,b and the Hirshfeld surface analysis made possible the recognition of the (oxadiazole)···(pyridine) and (oxadiazole)···(oxadiazole) interactions. The presence of these interactions was confirmed theoretically by DFT calculations, including NCI analysis for experimentally determined crystal structures as well as QTAIM analysis for optimized equilibrium structures. The preformed database survey allowed the verification of additional examples of relevant (oxadiazole)···π interactions both in Cambridge Structural Database and in Protein Data Bank, including the cocrystal of commercial anti-HIV drug Raltegravir.

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