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- PDB-2xex: crystal structure of Staphylococcus aureus elongation factor G -

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Basic information

Entry
Database: PDB / ID: 2xex
Titlecrystal structure of Staphylococcus aureus elongation factor G
ComponentsELONGATION FACTOR GEF-G
KeywordsTRANSLATION / GTPASE / BIOSYNTHETIC PROTEIN
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
: / Elongation factor G
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsChen, Y. / Koripella, R.K. / Sanyal, S. / Selmer, M.
CitationJournal: FEBS J. / Year: 2010
Title: Staphylococcus Aureus Elongation Factor G - Structure and Analysis of a Target for Fusidic Acid.
Authors: Chen, Y. / Koripella, R.K. / Sanyal, S. / Selmer, M.
History
DepositionMay 19, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,5486
Polymers153,3992
Non-polymers1494
Water9,170509
1
A: ELONGATION FACTOR G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7743
Polymers76,6991
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ELONGATION FACTOR G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7743
Polymers76,6991
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.160, 137.340, 125.360
Angle α, β, γ (deg.)90.00, 94.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 76699.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P68790
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.68 % / Description: NONE

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.9→46.2 Å / Num. obs: 110987 / % possible obs: 92.7 % / Observed criterion σ(I): 3.1 / Redundancy: 3.71 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.1 / % possible all: 78.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FNM

1fnm


Resolution: 1.9→46.2 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.506 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 4777 4.1 %RANDOM
Rwork0.187 ---
obs0.188 110987 92.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.13 Å20 Å2-1.19 Å2
2---1.87 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10352 0 4 509 10865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02210533
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.96514237
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04251330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89124.855484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87151851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6411560
X-RAY DIFFRACTIONr_chiral_restr0.1150.21595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217960
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9451.56627
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.672210684
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68533906
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.364.53553
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 300 -
Rwork0.299 6536 -
obs--78.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.01750.71340.53922.15610.30331.41880.1799-0.0567-0.15630.0883-0.0292-0.09490.268-0.0073-0.15070.0586-0.0068-0.03810.00370.00740.028135.1632-2.391365.8257
20.9433-0.04870.40122.57150.01652.4830.02810.0330.12370.0796-0.0616-0.1475-0.24160.04760.03350.0434-0.02340.03290.1011-0.02080.115747.933825.334963.6284
33.3657-0.28041.57592.92110.38936.6184-0.2371-0.60090.4490.34770.09540.0248-0.3373-0.41530.14160.08970.0410.01590.154-0.09110.125422.472136.036459.5039
41.13461.5252-0.77484.3879-2.57921.57610.0025-0.03750.04530.2797-0.0936-0.0525-0.25350.09830.09110.2554-0.0607-0.06450.07060.05730.066728.531351.032931.2062
50.47740.14080.22981.95290.19040.86480.0110.00350.0143-0.0462-0.0046-0.0235-0.06320.07-0.00640.0116-0.0110.01710.0742-0.00550.056620.500313.793342.3481
60.6196-0.21340.12761.8868-0.0791.5707-0.01170.04350.01460.02340.0418-0.0324-0.1372-0.0056-0.03010.03230.02540.00950.0432-0.00330.02215.658417.75530.1063
70.4775-0.15570.68953.11040.16863.32150.05360.0077-0.0883-0.0938-0.0292-0.21540.43140.1548-0.02440.10430.07590.02410.1154-0.04080.135728.3681-9.6061-4.0398
83.07912.05880.43053.03060.85133.9596-0.15790.2975-0.2775-0.38780.1730.09550.4972-0.3428-0.01510.1675-0.071-0.04940.0771-0.04130.10459.1061-20.607513.0412
91.7039-2.3030.26324.167-0.68520.32420.09750.0352-0.0558-0.2244-0.0310.21290.2092-0.0001-0.06650.19090.0293-0.02290.04440.0120.02428.8822-35.302733.3222
100.2389-0.12830.22212.29830.10861.37960.02030.0402-0.0477-0.0976-0.06160.0153-0.0308-0.02290.04130.0150.00340.00860.0559-0.00610.046616.06721.576928.096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 280
2X-RAY DIFFRACTION2A288 - 400
3X-RAY DIFFRACTION3A405 - 482
4X-RAY DIFFRACTION4A483 - 605
5X-RAY DIFFRACTION4A674 - 691
6X-RAY DIFFRACTION5A606 - 673
7X-RAY DIFFRACTION6B2 - 280
8X-RAY DIFFRACTION7B288 - 400
9X-RAY DIFFRACTION8B405 - 482
10X-RAY DIFFRACTION9B483 - 605
11X-RAY DIFFRACTION9B674 - 691
12X-RAY DIFFRACTION10B606 - 673

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