[English] 日本語
Yorodumi
- PDB-4hi0: Crystal Structure of Helicobacter pylori Urease Accessory Protein... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hi0
TitleCrystal Structure of Helicobacter pylori Urease Accessory Protein UreF/H/G complex
Components
  • Urease accessory protein UreF
  • Urease accessory protein UreG
  • Urease accessory protein UreH
KeywordsMETAL BINDING PROTEIN / Metallochaperone / Urease / Cytosol
Function / homology
Function and homology information


metabolic process / urea catabolic process / nickel cation binding / GTPase activity / GTP binding / identical protein binding / cytoplasm
Similarity search - Function
Urease accessory protein UreG / Urease accessory protein UreD / UreD urease accessory protein / Urease accessory protein UreF / Urease accessory protein UreF / Urease accessory protein UreF / UreF domain superfamily / UreF / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain ...Urease accessory protein UreG / Urease accessory protein UreD / UreD urease accessory protein / Urease accessory protein UreF / Urease accessory protein UreF / Urease accessory protein UreF / UreF domain superfamily / UreF / CobW/HypB/UreG, nucleotide-binding domain / CobW/HypB/UreG, nucleotide-binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Urease accessory protein UreF / Urease accessory protein UreG / Urease accessory protein UreH
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFong, Y.H. / Chen, Y.W. / Wong, K.B.
CitationJournal: Plos Biol. / Year: 2013
Title: Structure of UreG/UreF/UreH complex reveals how urease accessory proteins facilitate maturation of Helicobacter pylori urease.
Authors: Fong, Y.H. / Wong, H.C. / Yuen, M.H. / Lau, P.H. / Chen, Y.W. / Wong, K.B.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Urease accessory protein UreF
B: Urease accessory protein UreH
C: Urease accessory protein UreF
D: Urease accessory protein UreH
E: Urease accessory protein UreG
F: Urease accessory protein UreG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,6718
Polymers160,7856
Non-polymers8862
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18200 Å2
ΔGint-99 kcal/mol
Surface area48400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.124, 96.429, 237.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'B' and (resseq 6:260 )
211chain 'D' and (resseq 6:260 )
112chain 'A' and (resseq 28:254 )
212chain 'C' and (resseq 28:254 )
113chain 'E' and (resseq 1:196 )
213chain 'F' and (resseq 1:196 )

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Urease accessory protein UreF


Mass: 28651.834 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0069, ureF / Production host: Escherichia coli (E. coli) / References: UniProt: Q09065
#2: Protein Urease accessory protein UreH


Mass: 29757.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0067, ureH / Production host: Escherichia coli (E. coli) / References: UniProt: Q09067
#3: Protein Urease accessory protein UreG


Mass: 21983.334 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: HP_0068, ureG / Production host: Escherichia coli (E. coli) / References: UniProt: Q09066
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.5M ammonium sulfate, 100mM sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 15, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 72009 / Num. obs: 71616 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2
Reflection shellResolution: 2.35→2.49 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→29.875 Å / SU ML: 0.32 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2421 1922 2.78 %random
Rwork0.1915 ---
all0.1929 70969 --
obs0.1929 69047 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.242 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7198 Å20 Å2-0 Å2
2--6.0053 Å20 Å2
3----12.7251 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10646 0 56 303 11005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810890
X-RAY DIFFRACTIONf_angle_d1.18714714
X-RAY DIFFRACTIONf_dihedral_angle_d14.0934116
X-RAY DIFFRACTIONf_chiral_restr0.0821682
X-RAY DIFFRACTIONf_plane_restr0.0051890
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B2005X-RAY DIFFRACTIONPOSITIONAL
12D2005X-RAY DIFFRACTIONPOSITIONAL0.066
21A1809X-RAY DIFFRACTIONPOSITIONAL
22C1809X-RAY DIFFRACTIONPOSITIONAL0.051
31E1509X-RAY DIFFRACTIONPOSITIONAL
32F1509X-RAY DIFFRACTIONPOSITIONAL0.042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.3272850.24722858X-RAY DIFFRACTION57
2.4088-2.47390.31031290.24874548X-RAY DIFFRACTION90
2.4739-2.54660.31461330.23554617X-RAY DIFFRACTION92
2.5466-2.62880.32851300.24424664X-RAY DIFFRACTION92
2.6288-2.72270.3311380.24384742X-RAY DIFFRACTION94
2.7227-2.83160.33841410.22774864X-RAY DIFFRACTION96
2.8316-2.96040.30871370.22574917X-RAY DIFFRACTION97
2.9604-3.11630.25221420.22344984X-RAY DIFFRACTION98
3.1163-3.31130.2911450.21135050X-RAY DIFFRACTION99
3.3113-3.56660.24161450.20745064X-RAY DIFFRACTION99
3.5666-3.92480.20821460.17635087X-RAY DIFFRACTION99
3.9248-4.49110.21051480.14775160X-RAY DIFFRACTION100
4.4911-5.65210.18821470.15075168X-RAY DIFFRACTION99
5.6521-29.87720.18871560.17435402X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -23.7661 Å / Origin y: -10.9267 Å / Origin z: 38.3547 Å
111213212223313233
T0.1337 Å2-0.0063 Å20.0482 Å2-0.1488 Å2-0.0203 Å2--0.2192 Å2
L0.3082 °20.1475 °20.332 °2-0.3994 °20.3414 °2--2.1475 °2
S0.0567 Å °-0.1398 Å °0.053 Å °0.1204 Å °0.0178 Å °0.0095 Å °-0.2074 Å °-0.3058 Å °-0.0306 Å °
Refinement TLS groupSelection details: all

+
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