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- PDB-3t20: Crystal structure of Pseudomonas aeruginosa OccK5 (OpdH) -

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Basic information

Entry
Database: PDB / ID: 3t20
TitleCrystal structure of Pseudomonas aeruginosa OccK5 (OpdH)
ComponentsCis-aconitate porin OpdH
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
Cis-aconitate porin OpdH
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cis-aconitate porin OpdH


Theoretical massNumber of molelcules
Total (without water)44,3991
Polymers44,3991
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cis-aconitate porin OpdH

A: Cis-aconitate porin OpdH


Theoretical massNumber of molelcules
Total (without water)88,7992
Polymers88,7992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area1420 Å2
ΔGint-15 kcal/mol
Surface area34350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.106, 123.989, 114.349
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 Cis-aconitate porin OpdH


Mass: 44399.309 Da / Num. of mol.: 1 / Fragment: unp residues 37-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: opdH, PA0755 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5H4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 35% PEG 400, 0.1 M MgCl2, 50 mM Tris, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 15, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 18043 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.6→2.64 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→14.961 Å / SU ML: 0.92 / σ(F): 1.34 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2787 1913 10 %random
Rwork0.2154 ---
obs0.2218 18043 99.42 %-
all-19128 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.377 Å2 / ksol: 0.357 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.3554 Å20 Å20 Å2
2--16.5618 Å2-0 Å2
3---1.7935 Å2
Refinement stepCycle: LAST / Resolution: 2.6→14.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 0 97 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082931
X-RAY DIFFRACTIONf_angle_d1.2073953
X-RAY DIFFRACTIONf_dihedral_angle_d15.6971064
X-RAY DIFFRACTIONf_chiral_restr0.082413
X-RAY DIFFRACTIONf_plane_restr0.004517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5919-2.65640.43031230.31161119X-RAY DIFFRACTION93
2.6564-2.72780.321360.29421218X-RAY DIFFRACTION100
2.7278-2.80750.40371370.28441224X-RAY DIFFRACTION100
2.8075-2.89750.31941340.2571209X-RAY DIFFRACTION100
2.8975-3.00030.31231370.24091233X-RAY DIFFRACTION100
3.0003-3.11940.3081360.22241217X-RAY DIFFRACTION100
3.1194-3.25990.33021370.2261240X-RAY DIFFRACTION100
3.2599-3.42980.27251360.21651226X-RAY DIFFRACTION100
3.4298-3.64180.26431350.20651218X-RAY DIFFRACTION100
3.6418-3.91830.26131390.20641247X-RAY DIFFRACTION100
3.9183-4.30410.27191370.21031239X-RAY DIFFRACTION100
4.3041-4.90760.26541390.17571248X-RAY DIFFRACTION100
4.9076-6.11210.24511410.2041263X-RAY DIFFRACTION100
6.1121-14.96110.23361460.20451314X-RAY DIFFRACTION100

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