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- PDB-1ktv: Crystal Structure of Elongation Factor G Dimer Without Nucleotide -

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Basic information

Entry
Database: PDB / ID: 1ktv
TitleCrystal Structure of Elongation Factor G Dimer Without Nucleotide
ComponentsELONGATION FACTOR GEF-G
KeywordsTRANSLATION / apo form
Function / homology
Function and homology information


translational elongation / translation elongation factor activity / GDP binding / ribosome binding / GTPase activity / GTP binding / magnesium ion 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 speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsLaurberg, M. / Kristensen, O. / Su, X.D. / Liljas, A.
CitationJournal: To be Published
Title: A New Crystal Form of Thermus thermophilus Elongation Factor G Indicates Crystallographic Limitations Imposed on Molecular Flexibility
Authors: Laurberg, M. / Kristensen, O. / Su, X.D. / Liljas, A.
History
DepositionJan 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)153,9542
Polymers153,9542
Non-polymers00
Water0
1
A: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,9771
Polymers76,9771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ELONGATION FACTOR G


Theoretical massNumber of molelcules
Total (without water)76,9771
Polymers76,9771
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.987, 103.548, 176.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological entity is a monomer

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Components

#1: Protein ELONGATION FACTOR G / EF-G / EF-G


Mass: 76977.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: fus / Plasmid: pET13 (NOVAGEN) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P13551

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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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.02916 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02916 Å / Relative weight: 1
ReflectionResolution: 3.8→40 Å / Num. all: 14546 / Num. obs: 14546 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.184 / Net I/σ(I): 3.5
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique all: 1336 / % possible all: 100

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ELO

1elo


Resolution: 3.8→39.73 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 116835.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.374 674 5 %RANDOM
Rwork0.287 ---
all-14546 --
obs-13418 82.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.4648 Å2 / ksol: 0.303746 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.04 Å20 Å20 Å2
2---0.02 Å20 Å2
3----3.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.67 Å0.51 Å
Luzzati d res low-5 Å
Luzzati sigma a1.12 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 3.8→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9914 0 0 0 9914
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d1.37
LS refinement shellResolution: 3.8→4.04 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.403 115 5.8 %
Rwork0.338 1877 -
obs--75.3 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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