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- PDB-3zzt: Crystal structure of Staphylococcus aureus elongation factor G wi... -

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Basic information

Entry
Database: PDB / ID: 3zzt
TitleCrystal structure of Staphylococcus aureus elongation factor G with a fusidic-acid-resistant mutation F88L
ComponentsELONGATION FACTOR GEF-G
KeywordsTRANSLATION
Function / homology
Function and homology information


translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / Translation elongation factor EFG/EF2, domain IV ...Elongation Factor G (Translational Gtpase), domain 3 / Alpha-Beta Plaits - #240 / : / Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / Elongation Factor G, domain II / Elongation Factor G, domain III / Ribosomal Protein S5; domain 2 - #10 / 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 / Translation factors / EF-G domain III/V-like / Ribosomal Protein S5; domain 2 / 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. / Elongation Factor Tu (Ef-tu); domain 3 / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKoripella, R.K. / Chen, Y. / Selmer, M. / Sanyal, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Mechanism of Elongation Factor-G-Mediated Fusidic Acid Resistance and Fitness Compensation in Staphylococcus Aureus.
Authors: Koripella, R.K. / Chen, Y. / Peisker, K. / Koh, C.S. / Selmer, M. / Sanyal, S.
History
DepositionSep 5, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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


Theoretical massNumber of molelcules
Total (without water)153,3312
Polymers153,3312
Non-polymers00
Water41423
1
A: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,6651
Polymers76,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,6651
Polymers76,6651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.970, 127.930, 107.440
Angle α, β, γ (deg.)90.00, 107.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ELONGATION FACTOR G / EF-G / EF-G / 85 KDA VITRONECTIN-BINDING PROTEIN


Mass: 76665.273 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P68790
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 88 TO LEU ENGINEERED RESIDUE IN CHAIN B, PHE 88 TO LEU

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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: 2.65 Å3/Da / Density % sol: 54 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9538
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9538 Å / Relative weight: 1
ReflectionResolution: 2.95→47.4 Å / Num. obs: 32339 / % possible obs: 90.2 % / Observed criterion σ(I): 1.64 / Redundancy: 3.76 % / Biso Wilson estimate: 77.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.57
Reflection shellResolution: 2.95→3 Å / Redundancy: 3.79 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.64 / % possible all: 72.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FNM

1fnm


Resolution: 2.95→47.402 Å / SU ML: 1.03 / σ(F): 2.35 / Phase error: 36.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 1523 4.7 %
Rwork0.2409 --
obs0.2434 32326 90.28 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.463 Å2 / ksol: 0.264 e/Å3
Displacement parametersBiso mean: 93.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.4959 Å2-0 Å216.7304 Å2
2---10.6929 Å2-0 Å2
3---12.1889 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10036 0 0 23 10059
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410206
X-RAY DIFFRACTIONf_angle_d0.90313800
X-RAY DIFFRACTIONf_dihedral_angle_d14.823814
X-RAY DIFFRACTIONf_chiral_restr0.0651562
X-RAY DIFFRACTIONf_plane_restr0.0041806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.04520.4969900.40362288X-RAY DIFFRACTION73
3.0452-3.15410.40291030.36332412X-RAY DIFFRACTION77
3.1541-3.28030.39661330.32132542X-RAY DIFFRACTION83
3.2803-3.42960.39531500.30962681X-RAY DIFFRACTION88
3.4296-3.61030.35721330.29682845X-RAY DIFFRACTION91
3.6103-3.83640.35521500.27612901X-RAY DIFFRACTION94
3.8364-4.13250.30851550.25962925X-RAY DIFFRACTION94
4.1325-4.5480.25691420.20432997X-RAY DIFFRACTION97
4.548-5.20540.26771560.19323028X-RAY DIFFRACTION98
5.2054-6.55550.30051620.23833092X-RAY DIFFRACTION99
6.5555-47.40780.21341490.19363092X-RAY DIFFRACTION98

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