[English] 日本語
Yorodumi
- PDB-9uu2: Outer membrane protein OmpA-c-like domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9uu2
TitleOuter membrane protein OmpA-c-like domain
ComponentsMajor outer membrane protein
KeywordsSTRUCTURAL PROTEIN / Outer membrane protein OmpA-c-like domain
Function / homologyOuter membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / cell outer membrane / Major outer membrane protein
Function and homology information
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHe, J. / Gao, X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: A nonenzymatic effector disrupts Bacteroides cell wall homeostasis via OmpA targeting to mediate interbacterial competition
Authors: He, J. / Gao, X.
History
DepositionMay 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Major outer membrane protein


Theoretical massNumber of molelcules
Total (without water)11,9271
Polymers11,9271
Non-polymers00
Water73941
1
A: Major outer membrane protein

A: Major outer membrane protein


Theoretical massNumber of molelcules
Total (without water)23,8532
Polymers23,8532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area2080 Å2
ΔGint-15 kcal/mol
Surface area10290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.369, 44.369, 102.746
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

-
Components

#1: Protein Major outer membrane protein


Mass: 11926.585 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: During the experiment, author express the OmpA (BF9343_3708) protein using the truncation 286-395 fused to a C-terminal His-tag expression vector, however, during the structure analysis, the ...Details: During the experiment, author express the OmpA (BF9343_3708) protein using the truncation 286-395 fused to a C-terminal His-tag expression vector, however, during the structure analysis, the his-tag and D286 is not visible in the density map.
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: ompA, BF9343_3708 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5L8U3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 1% Tryptone, 0.001M sodium azide, 0.05M HEPES sodium pH 7.0, 20% w/v PEG3350.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 27, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.9→22.81 Å / Num. obs: 9756 / % possible obs: 99.64 % / Redundancy: 16.6 % / Biso Wilson estimate: 35.81 Å2 / Rrim(I) all: 0.127 / Net I/av σ(I): 37.769 / Net I/σ(I): 1.16
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 1.16 / Num. unique obs: 9756 / CC1/2: 0.762 / Rrim(I) all: 1.248

-
Processing

Software
NameVersionClassification
HKL-30007.21data scaling
PHENIX1.17.1_3660refinement
PHENIXphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.18 Å / SU ML: 0.2674 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.5813
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2483 975 10.01 %
Rwork0.213 8761 -
obs0.2167 9736 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.42 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 41 881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054855
X-RAY DIFFRACTIONf_angle_d0.73381155
X-RAY DIFFRACTIONf_chiral_restr0.0525130
X-RAY DIFFRACTIONf_plane_restr0.0058149
X-RAY DIFFRACTIONf_dihedral_angle_d5.6476120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.36611380.31181209X-RAY DIFFRACTION98.46
2-2.120.33221330.27211225X-RAY DIFFRACTION99.85
2.12-2.290.29461360.2381237X-RAY DIFFRACTION99.85
2.29-2.520.26021360.22731224X-RAY DIFFRACTION99.93
2.52-2.880.30561390.2411251X-RAY DIFFRACTION99.86
2.88-3.630.2681400.22691267X-RAY DIFFRACTION99.79
3.63-22.180.19281530.17631348X-RAY DIFFRACTION100

+
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