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- PDB-2y0l: Crystal Structure of Pseudomonas Aeruginosa OpdO -

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Basic information

Entry
Database: PDB / ID: 2y0l
TitleCrystal Structure of Pseudomonas Aeruginosa OpdO
ComponentsCIS-ACONITATE PORIN OPDH
KeywordsTRANSPORT PROTEIN / OUTER MEMBRANE / OPRD
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: 2.59 Å
AuthorsTouw, D.S. / Vijayaraghavan, J. / Vandenberg, B.
CitationJournal: To be Published
Title: Crystal Structure of Pseudomonas Aeruginosa Opdo
Authors: Touw, D.S. / Vijayaraghavan, J. / Vandenberg, B.
History
DepositionDec 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)44,4331
Polymers44,4331
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 / OPDO


Mass: 44433.492 Da / Num. of mol.: 1 / Fragment: MATURE PROTEIN, RESIDUES 26-427
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PB22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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
Sequence detailsAUTHORS INDICATE THAT THIS IS THE MATURE PROTEIN LACKING 25 RESIDUE SIGNAL PEPTIDE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 64 % / Description: NONE
Crystal growDetails: 0.1 M LITHIUM SULFATE, 0.05 M DISODIUM PHOSPHATE PH 4, 33% PEG 400.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 18242 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 10
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTK

2qtk


Resolution: 2.59→40.29 Å / SU ML: 0.4 / σ(F): 0 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.287 1823 10 %
Rwork0.22 --
obs0.227 18242 94.3 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.54 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.4961 Å20 Å20 Å2
2--16.2459 Å20 Å2
3---2.2502 Å2
Refinement stepCycle: LAST / Resolution: 2.59→40.29 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_d1.1773953
X-RAY DIFFRACTIONf_dihedral_angle_d15.9991064
X-RAY DIFFRACTIONf_chiral_restr0.078413
X-RAY DIFFRACTIONf_plane_restr0.004517
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5919-2.6620.44391100.2981042X-RAY DIFFRACTION80
2.662-2.74030.33771340.29471152X-RAY DIFFRACTION87
2.7403-2.82870.37251350.27071178X-RAY DIFFRACTION90
2.8287-2.92980.33561350.24631210X-RAY DIFFRACTION91
2.9298-3.0470.27661340.23311239X-RAY DIFFRACTION93
3.047-3.18570.32351390.23271268X-RAY DIFFRACTION95
3.1857-3.35350.30831390.21541281X-RAY DIFFRACTION97
3.3535-3.56350.28691440.20651294X-RAY DIFFRACTION98
3.5635-3.83850.26131510.2051321X-RAY DIFFRACTION98
3.8385-4.22440.2771470.21261329X-RAY DIFFRACTION99
4.2244-4.83480.26271490.17651338X-RAY DIFFRACTION99
4.8348-6.08790.2561480.21231354X-RAY DIFFRACTION99
6.0879-40.29670.26961580.24141413X-RAY DIFFRACTION98

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