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- PDB-8wv0: Outer membrane porin of Burkholderia pseudomallei (BpsOmp38) -

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Basic information

Entry
Database: PDB / ID: 8wv0
TitleOuter membrane porin of Burkholderia pseudomallei (BpsOmp38)
ComponentsOuter membrane porin (Fragment)
KeywordsPROTEIN TRANSPORT / Porin / Transport protein
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Porin, Neisseria sp. type / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / : / Porin domain superfamily
Similarity search - Domain/homology
Outer membrane porin
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBunkum, P. / Aunkham, A. / Bert van den, B. / Robinson, R.C. / Suginta, W.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Vidyasirimedhi Institute of Science and Technology (VISTEC) Thailand
CitationJournal: To Be Published
Title: Structure and function of outer membrane protein from Burkholderia pseudomallei (BpsOmp38)
Authors: Bunkum, P. / Aunkham, A. / Bert van den, B. / Robinson, R.C. / Suginta, W.
History
DepositionOct 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Outer membrane porin (Fragment)
A: Outer membrane porin (Fragment)
B: Outer membrane porin (Fragment)


Theoretical massNumber of molelcules
Total (without water)111,5683
Polymers111,5683
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.990, 98.900, 147.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Outer membrane porin (Fragment)


Mass: 37189.262 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: omp38 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): E. coli Omp8 Rosetta / References: UniProt: Q7WZL2
Has ligand of interestY
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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 33% v/v PEG 400, 0.1 M magnesium chloride, 0.1 M sodium chloride, 0.1 M Tris pH 8.5, and 5% water

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 1, 2015
RadiationMonochromator: LN2-Cooled, Fixed-Exit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→46.9 Å / Num. obs: 38930 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.027 / Rrim(I) all: 0.072 / Net I/σ(I): 3.51
Reflection shellResolution: 2.6→2.693 Å / Num. unique obs: 3830 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.11 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2744 1937 4.98 %
Rwork0.2474 --
obs0.2488 38930 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→44.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7421 0 0 0 7421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.595
X-RAY DIFFRACTIONf_dihedral_angle_d12.8432578
X-RAY DIFFRACTIONf_chiral_restr0.0431093
X-RAY DIFFRACTIONf_plane_restr0.0051376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.38561270.35752630X-RAY DIFFRACTION99
2.67-2.740.40671380.35162582X-RAY DIFFRACTION99
2.74-2.820.32371410.31882583X-RAY DIFFRACTION100
2.82-2.910.36121360.3082625X-RAY DIFFRACTION100
2.91-3.010.39991310.30432606X-RAY DIFFRACTION100
3.01-3.130.3671280.31592621X-RAY DIFFRACTION100
3.13-3.280.3851480.30362632X-RAY DIFFRACTION100
3.28-3.450.33141250.25452614X-RAY DIFFRACTION100
3.45-3.660.26581390.26022620X-RAY DIFFRACTION99
3.66-3.950.30191510.26162639X-RAY DIFFRACTION99
3.95-4.340.28881510.23642626X-RAY DIFFRACTION100
4.34-4.970.23151370.21162674X-RAY DIFFRACTION100
4.97-6.260.25031390.22972694X-RAY DIFFRACTION100
6.26-44.110.22491460.23462824X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 43.0985 Å / Origin y: 5.0664 Å / Origin z: -22.0544 Å
111213212223313233
T0.654 Å20.0188 Å2-0.0813 Å2-0.4804 Å2-0.0867 Å2--0.6471 Å2
L2.0332 °2-0.3926 °2-0.0962 °2-1.7981 °20.1589 °2--1.7852 °2
S-0.1262 Å °-0.0196 Å °0.12 Å °0.2548 Å °0.2657 Å °-0.1288 Å °-0.0975 Å °0.1442 Å °-0.126 Å °
Refinement TLS groupSelection details: all

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