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- PDB-9ga1: Structure of Pentameric Outer Membrane Protein A from Bdellovibri... -

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Basic information

Entry
Database: PDB / ID: 9ga1
TitleStructure of Pentameric Outer Membrane Protein A from Bdellovibrio bacteriovorus
ComponentsMajor outer membrane protein
KeywordsLIPID TRANSPORT / Outer Membrane Protein / Porin / Beta-barel
Function / homologybeta-D-glucopyranose / OCTAN-1-OL / N-OCTANE / PALMITIC ACID / Major outer membrane protein
Function and homology information
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsParr, R.J. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209437/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: A porin-like protein used by bacterial predator defines a wider lipid-trapping superfamily
Authors: Parr, R.J. / Lovering, A.L.
History
DepositionJul 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major outer membrane protein
B: Major outer membrane protein
C: Major outer membrane protein
D: Major outer membrane protein
E: Major outer membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,06828
Polymers181,4025
Non-polymers3,66623
Water5,314295
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29130 Å2
ΔGint-23 kcal/mol
Surface area65750 Å2
Unit cell
Length a, b, c (Å)175.430, 191.346, 184.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein / Sugars , 2 types, 9 molecules ABCDE

#1: Protein
Major outer membrane protein


Mass: 36280.457 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Gene: Bd0427 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6MQN4
#4: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 314 molecules

#2: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical
ChemComp-OCT / N-OCTANE


Mass: 114.229 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: C8H18
#5: Chemical
ChemComp-OC9 / OCTAN-1-OL


Mass: 130.228 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.26 Å3/Da / Density % sol: 71.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1M NaCl, 25% v/v pentaerythritol propoxylate (5/4 PO/OH), 10% v/v DMSO

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.8→63.54 Å / Num. obs: 76317 / % possible obs: 99.89 % / Redundancy: 13.9 % / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.1614 / Rpim(I) all: 0.0448 / Rrim(I) all: 0.1675 / Net I/σ(I): 12.26
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 1.48 / Num. unique obs: 7548 / CC1/2: 0.871 / CC star: 0.965 / Rpim(I) all: 0.2795 / Rrim(I) all: 1.05 / % possible all: 99.96

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
DIALSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→63.54 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 3737 4.9 %
Rwork0.1977 --
obs0.1998 76238 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→63.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12620 0 250 295 13165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813141
X-RAY DIFFRACTIONf_angle_d0.98317756
X-RAY DIFFRACTIONf_dihedral_angle_d10.2751921
X-RAY DIFFRACTIONf_chiral_restr0.0541949
X-RAY DIFFRACTIONf_plane_restr0.0062322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.840.42991170.33992694X-RAY DIFFRACTION100
2.84-2.870.36391430.29252642X-RAY DIFFRACTION100
2.87-2.910.33941320.28112654X-RAY DIFFRACTION100
2.91-2.950.36461500.25662681X-RAY DIFFRACTION100
2.95-30.30351240.25542638X-RAY DIFFRACTION100
3-3.040.28361290.20452674X-RAY DIFFRACTION100
3.04-3.090.24641310.18622682X-RAY DIFFRACTION100
3.09-3.150.27481330.18452674X-RAY DIFFRACTION100
3.15-3.210.25171250.18842644X-RAY DIFFRACTION100
3.21-3.270.2341210.18522705X-RAY DIFFRACTION100
3.27-3.330.26931220.19532681X-RAY DIFFRACTION100
3.33-3.410.25071280.20152687X-RAY DIFFRACTION100
3.41-3.490.2441370.20732667X-RAY DIFFRACTION100
3.49-3.570.25071310.2162685X-RAY DIFFRACTION100
3.57-3.670.29841390.21942658X-RAY DIFFRACTION100
3.67-3.780.24821420.2052671X-RAY DIFFRACTION100
3.78-3.90.28711470.1942690X-RAY DIFFRACTION100
3.9-4.040.22971460.18542677X-RAY DIFFRACTION100
4.04-4.20.20341430.17112672X-RAY DIFFRACTION100
4.2-4.390.18721480.16432684X-RAY DIFFRACTION100
4.39-4.620.20161510.15692694X-RAY DIFFRACTION100
4.62-4.910.19211590.15642675X-RAY DIFFRACTION100
4.91-5.290.18481720.1592661X-RAY DIFFRACTION100
5.29-5.820.21591350.17012724X-RAY DIFFRACTION100
5.82-6.660.23771270.18582748X-RAY DIFFRACTION100
6.66-8.390.22161540.19382745X-RAY DIFFRACTION100
8.39-63.540.23061510.26592794X-RAY DIFFRACTION98

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