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- PDB-7cdw: Crystal Structure of Mycobacterium Tuberculosis Elongation Factor G1 -

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Basic information

Entry
Database: PDB / ID: 7cdw
TitleCrystal Structure of Mycobacterium Tuberculosis Elongation Factor G1
ComponentsElongation factor GEF-G
KeywordsHYDROLASE / GTPase / Elongation factor G(EF-G) / Ribosome-bound EF-G / Crystal structure / Antituberculosis drugs
Function / homology
Function and homology information


ribosome disassembly / cell wall / translation elongation factor activity / GTPase activity / GTP binding / plasma membrane / cytosol
Similarity search - Function
Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like ...Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Translation elongation factor EFG/EF2, domain IV / Elongation factor G, domain IV / Elongation factor G, domain IV / Elongation factor G C-terminus / Elongation factor EFG, domain V-like / Elongation factor G C-terminus / EF-G domain III/V-like / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Elongation factor G
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsGao, X. / Cui, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81572005 China
CitationJournal: Front Mol Biosci / Year: 2021
Title: Crystal Structure of Mycobacterium tuberculosis Elongation Factor G1.
Authors: Gao, X. / Yu, X. / Zhu, K. / Qin, B. / Wang, W. / Han, P. / Aleksandra Wojdyla, J. / Wang, M. / Cui, S.
History
DepositionJun 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongation factor G
B: Elongation factor G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,5084
Polymers158,6212
Non-polymers8862
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-29 kcal/mol
Surface area59570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.543, 301.516, 145.865
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Elongation factor G / EF-G / EF-G


Mass: 79310.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: fusA, Rv0684, MTCY210.01, MTV040.12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P9WNM7
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 20mM magnesium chloride,50mM MOPS pH 7.0,55%TacsimateTM pH 7.0 and 5mM Hexammine cobalt(III) chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3→48.85 Å / Num. obs: 83429 / % possible obs: 96.7 % / Redundancy: 2.92 % / CC1/2: 0.996 / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.73
Reflection shellResolution: 3→3.19 Å / Redundancy: 2.88 % / Mean I/σ(I) obs: 2.37 / Num. unique obs: 13613 / CC1/2: 0.812 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3→47.95 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 3800 4.56 %
Rwork0.2062 79592 -
obs0.2078 83392 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 520.25 Å2 / Biso mean: 75.2957 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3→47.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10537 0 76 0 10613
Biso mean--55.37 --
Num. residues----1361
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.040.33521400.32752924306494
3.04-3.080.3681430.30653006314998
3.08-3.120.34451440.28583037318199
3.12-3.170.35091440.29512979312398
3.17-3.220.3261400.28862935307599
3.22-3.270.3461370.26743013315099
3.27-3.320.27331440.26893046319098
3.32-3.380.29011470.24193005315298
3.38-3.440.28011430.24492944308798
3.44-3.50.32431420.23373022316498
3.5-3.580.2881380.22722972311098
3.58-3.650.26991430.22123013315698
3.65-3.740.28251400.2262995313598
3.74-3.830.24251420.21252918306097
3.83-3.940.23481370.20473003314097
3.94-4.050.24861410.19383007314897
4.05-4.180.21951400.18472898303897
4.18-4.330.23751460.17532944309097
4.33-4.510.22591340.16092926306096
4.51-4.710.19811440.15162950309496
4.71-4.960.17231440.16042900304496
4.96-5.270.22781370.17262906304395
5.27-5.670.18391410.20282917305895
5.68-6.240.19511340.21422826296094
6.25-7.150.19711420.21692907304995
7.15-8.990.20061370.17542842297993
8.99-47.950.21451360.17752757289390
Refinement TLS params.Method: refined / Origin x: 27.4812 Å / Origin y: 193.0424 Å / Origin z: 71.4925 Å
111213212223313233
T0.4228 Å20.0161 Å2-0.004 Å2-0.4769 Å2-0.0388 Å2--0.47 Å2
L0.1524 °2-0.0476 °20.1793 °2-0.5516 °2-0.1957 °2--0.2937 °2
S0.0093 Å °0.0239 Å °0.023 Å °0.0131 Å °-0.0405 Å °0.0389 Å °-0.0199 Å °0.072 Å °0.0302 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 701
2X-RAY DIFFRACTION1allB4 - 701
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allD1

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