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- PDB-2qtk: Crystal Structure of the outer membrane protein opdK from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 2qtk
TitleCrystal Structure of the outer membrane protein opdK from Pseudomonas aeruginosa
ComponentsProbable porin
KeywordsMEMBRANE PROTEIN / Outer membrane protein / beta barrel / vanillate transport / Porin
Function / homology
Function and homology information


porin activity / membrane
Similarity search - Function
Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Vanillate porin OpdK
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsBiswas, S. / Van den Berg, B.
CitationJournal: Structure / Year: 2008
Title: Crystal Structure of the Outer Membrane Protein OpdK from Pseudomonas aeruginosa.
Authors: Biswas, S. / Mohammad, M.M. / Movileanu, L. / van den Berg, B.
History
DepositionAug 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable porin
B: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,72924
Polymers85,9872
Non-polymers6,74222
Water00
1
A: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,67113
Polymers42,9941
Non-polymers3,67712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,05811
Polymers42,9941
Non-polymers3,06410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.889, 96.697, 121.411
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is monomer of OpdK

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Components

#1: Protein Probable porin


Mass: 42993.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Protein expression under the control of the arabinose promoter
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: Pseudomonas aeruginosa
Plasmid: OpdK gene with ShlB signal sequence cloned into pB22 with 8 His tag
Production host: Escherichia coli (E. coli) / Strain (production host): C43 E.Coli cells / References: UniProt: Q9HUR5
#2: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM

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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: 2.8 Å3/Da / Density % sol: 55.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Classic screen condition #87 from Nextal, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2007 / Details: Platinum coated mirror
RadiationMonochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 23772 / Num. obs: 23167 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 20.4 Å2 / Net I/σ(I): 18.29
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 2.7 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2951 1826 -Random
Rwork0.2334 ---
all0.2334 23470 --
obs0.2334 23167 97.4 %-
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5795 0 273 0 6068
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
LS refinement shellResolution: 2.8→2.94 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.328 203 -
Rwork0.287 --
obs-2614 90.1 %

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