[English] 日本語
Yorodumi
- PDB-5tv2: Crystal structure of a fragment (1-405) of an elongation factor G... -

+
Open data


ID or keywords:

Loading...

-
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 GEF-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


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 / 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 ...Translation elongation factor EFG/EF2 / Elongation factor G, domain III / EFG, domain V / 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 / Translation factors / 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 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: To Be Published
Title: Crystal structure of a fragment (1-405) of an elongation factor G from Vibrio vulnificus CMCP6
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

#1: Protein Elongation factor G / EF-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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more