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- PDB-3t0s: Crystal structure of Pseudomonas aeruginosa OccK4 (OpdL) -

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Basic information

Entry
Database: PDB / ID: 3t0s
TitleCrystal structure of Pseudomonas aeruginosa OccK4 (OpdL)
Componentsporin
KeywordsMEMBRANE PROTEIN / beta-barrel / channel / bacterial outer membrane
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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Authorsvan den Berg, B. / Eren, E.
CitationJournal: Plos Biol. / Year: 2012
Title: Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
Authors: Eren, E. / Vijayaraghavan, J. / Liu, J. / Cheneke, B.R. / Touw, D.S. / Lepore, B.W. / Indic, M. / Movileanu, L. / van den Berg, B.
History
DepositionJul 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,86215
Polymers44,5721
Non-polymers4,29014
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.227, 115.032, 100.632
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein porin


Mass: 44571.625 Da / Num. of mol.: 1 / Fragment: unp residues 28-418
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA4137 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HWP4
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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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: 2.96 Å3/Da / Density % sol: 58.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 30% PEG400 50 mM NaCl 0.1 M Na-citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 29, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 29467 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.03 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.693 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 23.25 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 1289 5.26 %random
Rwork0.2124 ---
all0.214 24521 --
obs0.2143 24521 90.14 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.506 Å2 / ksol: 0.409 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7505 Å20 Å2-0 Å2
2--8.1841 Å20 Å2
3----5.4336 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 97 119 3078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073008
X-RAY DIFFRACTIONf_angle_d1.0884028
X-RAY DIFFRACTIONf_dihedral_angle_d15.891119
X-RAY DIFFRACTIONf_chiral_restr0.075422
X-RAY DIFFRACTIONf_plane_restr0.004515
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2880.27511300.22522450X-RAY DIFFRACTION86
2.288-2.39190.26311470.21672457X-RAY DIFFRACTION87
2.3919-2.51780.25921350.21752526X-RAY DIFFRACTION89
2.5178-2.67520.28821530.20882560X-RAY DIFFRACTION91
2.6752-2.88120.27421390.22262627X-RAY DIFFRACTION92
2.8812-3.170.26851480.21412672X-RAY DIFFRACTION94
3.17-3.62630.26571450.20372653X-RAY DIFFRACTION93
3.6263-4.55930.21631510.2012646X-RAY DIFFRACTION91
4.5593-19.69390.22931410.22262641X-RAY DIFFRACTION88

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