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- PDB-8jto: Outer membrane porin of Burkholderia pseudomallei (BpsOmp38) in c... -

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Basic information

Entry
Database: PDB / ID: 8jto
TitleOuter membrane porin of Burkholderia pseudomallei (BpsOmp38) in complex with ceftazidime
ComponentsOuter membrane porin (Fragment)
KeywordsPROTEIN TRANSPORT / Burkholderia pseudomallei / Outer membrane protein / 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: 2.25 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
DepositionJun 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane porin (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,82212
Polymers38,0181
Non-polymers2,80411
Water1,71195
1
A: Outer membrane porin (Fragment)
hetero molecules

A: Outer membrane porin (Fragment)
hetero molecules

A: Outer membrane porin (Fragment)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,46636
Polymers114,0543
Non-polymers8,41233
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area16120 Å2
ΔGint-156 kcal/mol
Surface area40330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.045, 151.045, 49.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-410-

NA

21A-411-

NA

31A-591-

HOH

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Components

#1: Protein Outer membrane porin (Fragment)


Mass: 38018.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: omp38 / Production host: Escherichia coli (E. coli) / Strain (production host): E.coli C43 (DE3) / References: UniProt: Q7WZL2
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: C8E, detergent*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.25 Å3/Da / Density % sol: 71.08 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.5 M Sodium Chloride, 0.05 M Calcium Chloride dihydrate, 0.1 M MES, pH6.5, and 37% w/v PEG 400

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2020 / Details: LN2-Cooled, Fixed-Exit
RadiationMonochromator: LN2-Cooled, Fixed-Exit / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.249→19.95 Å / Num. obs: 27951 / % possible obs: 87.4 % / Redundancy: 2.3 % / CC1/2: 0.993 / CC star: 0.998 / Net I/σ(I): 11.1
Reflection shellResolution: 2.25→2.25 Å / Num. unique obs: 30807 / CC1/2: 0.832

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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: 2.25→19.95 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1359 4.87 %
Rwork0.1866 --
obs0.1883 27926 90.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 9 95 2751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d0.749
X-RAY DIFFRACTIONf_dihedral_angle_d17.564434
X-RAY DIFFRACTIONf_chiral_restr0.05379
X-RAY DIFFRACTIONf_plane_restr0.006480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.330.2351170.1972120X-RAY DIFFRACTION74
2.33-2.420.22371310.19022508X-RAY DIFFRACTION87
2.42-2.530.23881410.1972621X-RAY DIFFRACTION91
2.53-2.670.24051250.19252612X-RAY DIFFRACTION89
2.67-2.830.24881510.19262755X-RAY DIFFRACTION95
2.83-3.050.22031420.19332814X-RAY DIFFRACTION96
3.05-3.360.21411390.18072795X-RAY DIFFRACTION96
3.36-3.840.20681400.182782X-RAY DIFFRACTION95
3.84-4.820.22061590.18542743X-RAY DIFFRACTION94
4.83-19.950.22591140.18392817X-RAY DIFFRACTION92

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