[English] 日本語
Yorodumi
- PDB-2hjg: The crystal structure of the B. subtilis YphC GTPase in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hjg
TitleThe crystal structure of the B. subtilis YphC GTPase in complex with GDP
ComponentsGTP-binding protein engA
KeywordsHYDROLASE / GTPase EngA KH-domain
Function / homology
Function and homology information


ribosome binding / ribosome biogenesis / GTP binding
Similarity search - Function
GTP-binding protein EngA / EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta ...GTP-binding protein EngA / EngA-type guanine nucleotide-binding (G) domain / EngA-type guanine nucleotide-binding (G) domain profile. / GTPase Der, C-terminal KH-domain-like / KH-domain-like of EngA bacterial GTPase enzymes, C-terminal / K homology (KH) domain / 50S ribosome-binding GTPase / GTP binding domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase Der
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMuench, S.P. / Xu, L. / Sedelnikova, S.E. / Rice, D.W.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The essential GTPase YphC displays a major domain rearrangement associated with nucleotide binding.
Authors: Muench, S.P. / Xu, L. / Sedelnikova, S.E. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Cloning, purification and preliminary crystallographic analysis of the Bacillus subtilis GTPase YphC-GDP complex.
Authors: Xu, L. / Muench, S.P. / Roujeinikova, A. / Sedelnikova, S.E. / Rice, D.W.
History
DepositionJun 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP-binding protein engA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3434
Polymers49,3911
Non-polymers9523
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.711, 65.045, 110.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

-
Components

#1: Protein GTP-binding protein engA


Mass: 49391.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: engA / Plasmid: pMAT1 / Production host: Escherichia coli (E. coli) / Strain (production host): E. coli Tuner (DE3) / References: UniProt: P50743
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M sodium flouride, 20% (w/v) PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.9794, 0.9797, 1.0094
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 27, 2005
RadiationMonochromator: double crystal Si(III)monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97971
31.00941
ReflectionResolution: 2.5→30 Å / Num. obs: 16253 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.1 / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.96 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.895 / SU B: 22.068 / SU ML: 0.232 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.319 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27353 814 5 %RANDOM
Rwork0.21539 ---
obs0.21815 15364 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.463 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2---0.61 Å20 Å2
3---2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 57 31 3235
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223266
X-RAY DIFFRACTIONr_bond_other_d0.0060.022974
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9774431
X-RAY DIFFRACTIONr_angle_other_deg0.76636902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.2835395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4224.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.34615554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11519
X-RAY DIFFRACTIONr_chiral_restr0.0710.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023573
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02655
X-RAY DIFFRACTIONr_nbd_refined0.2020.2670
X-RAY DIFFRACTIONr_nbd_other0.1960.22930
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21593
X-RAY DIFFRACTIONr_nbtor_other0.0830.21768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.274
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2961.52132
X-RAY DIFFRACTIONr_mcbond_other0.0621.5809
X-RAY DIFFRACTIONr_mcangle_it0.81623221
X-RAY DIFFRACTIONr_scbond_it1.86331414
X-RAY DIFFRACTIONr_scangle_it2.6444.51210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 67 -
Rwork0.254 1076 -
obs--100 %

+
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