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

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Basic information

Entry
Database: PDB / ID: 3zzu
TitleCrystal structure of Staphylococcus aureus elongation factor G with mutations M16I and 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: 2.98 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 / Derived calculations / 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 / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BD" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ELONGATION FACTOR G
B: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)153,2942
Polymers153,2942
Non-polymers00
Water543
1
A: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,6471
Polymers76,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,6471
Polymers76,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.200, 125.520, 106.900
Angle α, β, γ (deg.)90.00, 108.21, 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: 76647.234 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.: 3 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, MET 16 TO ILE ENGINEERED RESIDUE IN CHAIN A, PHE 88 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, MET 16 TO ILE ENGINEERED RESIDUE IN CHAIN A, PHE 88 TO LEU ENGINEERED RESIDUE IN CHAIN B, MET 16 TO ILE 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: 2.98→47.2 Å / Num. obs: 31218 / % possible obs: 93.2 % / Observed criterion σ(I): 1.8 / Redundancy: 3.7 % / Biso Wilson estimate: 94.45 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.13
Reflection shellResolution: 2.98→3 Å / Redundancy: 3.83 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.8 / % possible all: 76.4

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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: 2.98→47.147 Å / SU ML: 1.04 / σ(F): 2.35 / Phase error: 35.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2942 1480 4.7 %
Rwork0.237 --
obs0.2397 31201 93.28 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 85.876 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 115.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.2373 Å20 Å211.2253 Å2
2---6.5349 Å20 Å2
3---6.7722 Å2
Refinement stepCycle: LAST / Resolution: 2.98→47.147 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10036 0 0 3 10039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410206
X-RAY DIFFRACTIONf_angle_d0.93713802
X-RAY DIFFRACTIONf_dihedral_angle_d15.6293812
X-RAY DIFFRACTIONf_chiral_restr0.0691564
X-RAY DIFFRACTIONf_plane_restr0.0041806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.07620.42081000.35562248X-RAY DIFFRACTION78
3.0762-3.18610.44861270.3462442X-RAY DIFFRACTION85
3.1861-3.31360.37811290.33322564X-RAY DIFFRACTION89
3.3136-3.46440.38751380.30882688X-RAY DIFFRACTION93
3.4644-3.6470.3811270.29812753X-RAY DIFFRACTION95
3.647-3.87540.34851420.27642744X-RAY DIFFRACTION96
3.8754-4.17450.29111510.24262820X-RAY DIFFRACTION98
4.1745-4.59420.27181340.20212877X-RAY DIFFRACTION99
4.5942-5.25830.24811430.1982873X-RAY DIFFRACTION99
5.2583-6.62190.33171500.25562889X-RAY DIFFRACTION99
6.6219-47.15310.22671390.19252823X-RAY DIFFRACTION95

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