[English] 日本語
Yorodumi
- PDB-5j4g: Crystal structure of the C-terminally His6-tagged HP0902, an unch... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5j4g
TitleCrystal structure of the C-terminally His6-tagged HP0902, an uncharacterized protein from Helicobacter pylori 26695
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / HP0902 / Helicobacter pylori / secretory protein / Cupin family / Uncharacterized protein
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / Cupin type-2 domain-containing protein
Function and homology information
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSim, D.W. / Lee, W.C. / Kim, H.Y. / Kim, J.H. / Won, H.S.
Citation
Journal: FEBS Lett. / Year: 2016
Title: Structural identification of the lipopolysaccharide-binding capability of a cupin-family protein from Helicobacter pylori
Authors: Sim, D.W. / Kim, J.H. / Kim, H.Y. / Jang, J.H. / Lee, W.C. / Kim, E.H. / Park, P.J. / Lee, K.H. / Won, H.S.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2011
Title: Crystallization and X-ray data collection of HP0902 from Helicobacter pylori 26695
Authors: Sim, D.W. / Song, J.H. / Lee, W.C. / Lee, Y.S. / Kim, H.Y. / Won, H.S.
History
DepositionApr 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)24,2382
Polymers24,2382
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-5 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.355, 50.355, 142.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Uncharacterized protein


Mass: 12119.166 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: C-terminal 6xHis tag
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: HP_0902 / Production host: Escherichia coli (E. coli) / References: UniProt: O25562
#2: Water ChemComp-HOH / 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: 1.86 Å3/Da / Density % sol: 33.77 % / Description: short needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 3350, ammonium acetate, bis-tris

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 12, 2010
RadiationMonochromator: Cryo-cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→71 Å / Num. obs: 6158 / % possible obs: 98.2 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 39.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
MOSFLMdata processing
SCALAdata scaling
MOLREPphasing
SHELXDEmodel building
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q30

2q30


Resolution: 2.6→41.076 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 11.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 280 4.6 %Random selection
Rwork0.1824 ---
obs0.1856 6093 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→41.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1524 0 0 31 1555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111544
X-RAY DIFFRACTIONf_angle_d1.3542071
X-RAY DIFFRACTIONf_dihedral_angle_d18.023964
X-RAY DIFFRACTIONf_chiral_restr0.076244
X-RAY DIFFRACTIONf_plane_restr0.008263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6004-3.2760.33111450.20642814X-RAY DIFFRACTION100
3.276-41.08150.21431350.17082999X-RAY DIFFRACTION99

+
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