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- PDB-9uu2: Outer membrane protein OmpA-c-like domain -

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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. / Chen, Z. / Jiang, K. / Yang, Y. / Li, W. / Wang, X. / Xu, X. / Zheng, S. / Jiao, X. / Chen, X. / Huo, L. / Lim, B. / Liu, S.J. / Gao, X.
History
DepositionMay 5, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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.

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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

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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

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