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- PDB-5tv2: Crystal structure of a fragment (1-405) of an elongation factor G... -

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Basic information

Entry
Database: PDB / ID: 5tv2
TitleCrystal structure of a fragment (1-405) of an elongation factor G from Vibrio vulnificus CMCP6
ComponentsElongation factor G
KeywordsNUCLEAR PROTEIN / GTP-binding domain / domain II / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / TRANSFERASE
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Translation factors / 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 ...Translation elongation factor EFG/EF2 / : / Elongation factor G, domain III / EFG, domain V / Translation factors / 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 (Ef-tu); domain 3 / 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 / P-loop containing nucleotide triphosphate hydrolases / Ribosomal protein S5 domain 2-type fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionNov 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_prerelease_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Feb 11, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor G


Theoretical massNumber of molelcules
Total (without water)45,2611
Polymers45,2611
Non-polymers00
Water4,414245
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.678, 54.496, 65.319
Angle α, β, γ (deg.)90.00, 116.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Elongation factor G / EF-G


Mass: 45260.984 Da / Num. of mol.: 1 / Fragment: residues 1-405
Source method: isolated from a genetically manipulated source
Details: Protein degraded during crystallization. Only part of the protein was crystallized.
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: fusA, VV1_1338 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q8DCQ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 245 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 MMT buffer, 25 % PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2016 / Details: 3.0 Undulator
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 48492 / % possible obs: 97.8 % / Redundancy: 6.4 % / CC1/2: 0.75 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2460 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4fn5

4fn5


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.746 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.108 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25307 2405 5 %RANDOM
Rwork0.17864 ---
obs0.18232 46069 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.817 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å2-2.01 Å2
2--2.8 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 0 247 3109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192933
X-RAY DIFFRACTIONr_bond_other_d0.0020.022819
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.953967
X-RAY DIFFRACTIONr_angle_other_deg0.97736472
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4195366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.8424.583144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25315521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7341523
X-RAY DIFFRACTIONr_chiral_restr0.1180.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.023342
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02657
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_it4.2572.2611470
X-RAY DIFFRACTIONr_mcbond_other4.26920.9421469
X-RAY DIFFRACTIONr_mcangle_it4.9963.3921834
X-RAY DIFFRACTIONr_mcangle_other4.9951835
X-RAY DIFFRACTIONr_scbond_it6.0882.7751463
X-RAY DIFFRACTIONr_scbond_other6.071461
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.82819.0212133
X-RAY DIFFRACTIONr_long_range_B_refined6.6053276
X-RAY DIFFRACTIONr_long_range_B_other6.563221
X-RAY DIFFRACTIONr_rigid_bond_restr4.28732933
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded18.56652888
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 165 -
Rwork0.264 3340 -
obs--95.84 %
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)
11.3955-0.7202-0.30511.01330.80864.9544-0.0023-0.1142-0.1119-0.09120.1172-0.0152-0.21910.0125-0.11490.04620.00290.04710.01860.01430.05921.0736-0.9562-0.0326
21.34440.4620.52721.3133-0.37291.011-0.1889-0.22410.13210.25120.13430.0169-0.2159-0.20930.05460.15030.09810.02970.0819-0.01370.098421.65454.8359.3288
31.92030.7010.26811.96690.29182.1573-0.1682-0.39480.06640.41530.12520.0573-0.0319-0.09550.04310.17340.10830.03420.1284-0.01480.045625.8252-1.203123.1084
41.54371.91250.51165.92491.84540.7935-0.0228-0.2045-0.19690.5244-0.0032-0.02190.2991-0.15770.0260.2056-0.00510.070.23890.05980.076627.4198-19.510623.9686
50.8529-0.12270.38131.3172-0.4950.6539-0.1623-0.3347-0.07070.16160.17780.105-0.0352-0.223-0.01550.09350.07010.08060.14850.03290.094922.8087-6.693513.0116
62.11470.83590.34641.6157-0.22230.9564-0.0554-0.00570.0257-0.07720.12560.22470.003-0.139-0.07020.0171-0.00430.02010.02590.02450.10397.47675.848-7.3425
72.02150.50410.50991.8556-0.45141.5444-0.03180.08830.0798-0.13260.07090.24580.0167-0.0554-0.03910.0322-0.00170.02330.00850.01330.10799.36226.7703-8.1668
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 23
2X-RAY DIFFRACTION2A24 - 124
3X-RAY DIFFRACTION3A125 - 209
4X-RAY DIFFRACTION4A210 - 242
5X-RAY DIFFRACTION5A243 - 296
6X-RAY DIFFRACTION6A297 - 367
7X-RAY DIFFRACTION7A368 - 405

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