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- PDB-2y0h: Crystal Structure of Pseudomonas Aeruginosa OpdL -

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Basic information

Entry
Database: PDB / ID: 2y0h
TitleCrystal Structure of Pseudomonas Aeruginosa OpdL
ComponentsPROBABLE PORIN
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
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTouw, D.S. / Vijayaraghavan, J. / Vandenberg, B.
CitationJournal: To be Published
Title: Crystal Structure of Pseudomonas Aeruginosa Opdl
Authors: Touw, D.S. / Vijayaraghavan, J. / Vandenberg, B.
History
DepositionDec 2, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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: PROBABLE PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,61214
Polymers43,6291
Non-polymers3,98413
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 PROBABLE PORIN / OPDL


Mass: 43628.652 Da / Num. of mol.: 1 / Fragment: RESIDUES 28-418
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: Q9HWP4
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 13 / 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: 3.1 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growDetails: 28% PEG 400, 0.05M SODIUM CITRATE, PH 5.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1
DetectorType: MARRESEARCH QUANTUM 210 / Detector: CCD / Date: Oct 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 34444 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Biso Wilson estimate: 34.23 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 2→2.03 Å / Redundancy: 5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTK

2qtk


Resolution: 2.2→19.69 Å / SU ML: 0.3 / σ(F): 0 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.249 1289 5.3 %
Rwork0.212 --
obs0.214 24521 90.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.51 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.7699 Å20 Å20 Å2
2--8.1948 Å20 Å2
3----5.4249 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 0 85 119 3066
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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