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- PDB-3syb: Crystal structure of Pseudomonas aeruginosa OccD3 (OpdP) -

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Basic information

Entry
Database: PDB / ID: 3syb
TitleCrystal structure of Pseudomonas aeruginosa OccD3 (OpdP)
ComponentsGlycine-glutamate dipeptide porin OpdP
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
Glycine-glutamate dipeptide porin OpdP
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / P / Resolution: 2.7 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 16, 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: Glycine-glutamate dipeptide porin OpdP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5696
Polymers51,4571
Non-polymers1,1115
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Glycine-glutamate dipeptide porin OpdP
hetero molecules

A: Glycine-glutamate dipeptide porin OpdP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,13712
Polymers102,9152
Non-polymers2,22310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3750 Å2
ΔGint-53 kcal/mol
Surface area35640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.930, 159.828, 82.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-489-

HOH

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Components

#1: Protein Glycine-glutamate dipeptide porin OpdP


Mass: 51457.297 Da / Num. of mol.: 1 / Fragment: unp residues 26-484
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: opdP, PA4501 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVS0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


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


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.18 Å3/Da / Density % sol: 61.37 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 25% PEG 1000 0.2 M ammonium sulphate 50 mM Na-citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 17, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 18213 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.66→2.71 Å / % possible all: 96.5

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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: P / Resolution: 2.7→9.993 Å / SU ML: 0.76 / σ(F): 1.34 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2671 1802 10.01 %random
Rwork0.2141 ---
obs0.2194 18004 99.93 %-
all-18004 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.632 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3442 Å20 Å2-0 Å2
2--16.4879 Å20 Å2
3----11.1438 Å2
Refinement stepCycle: LAST / Resolution: 2.7→9.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3157 0 41 45 3243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083270
X-RAY DIFFRACTIONf_angle_d1.1634432
X-RAY DIFFRACTIONf_dihedral_angle_d16.7091142
X-RAY DIFFRACTIONf_chiral_restr0.075465
X-RAY DIFFRACTIONf_plane_restr0.004579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.77150.35681340.27151241X-RAY DIFFRACTION100
2.7715-2.85120.36681390.25531216X-RAY DIFFRACTION100
2.8512-2.9410.31571380.24871230X-RAY DIFFRACTION100
2.941-3.04330.29011310.21831251X-RAY DIFFRACTION100
3.0433-3.16140.28021360.21151220X-RAY DIFFRACTION100
3.1614-3.30030.32661380.22311219X-RAY DIFFRACTION100
3.3003-3.46740.25021390.22951244X-RAY DIFFRACTION100
3.4674-3.67450.26981380.21611242X-RAY DIFFRACTION100
3.6745-3.94190.24951430.21741254X-RAY DIFFRACTION100
3.9419-4.30950.24291360.19391254X-RAY DIFFRACTION100
4.3095-4.86890.24121390.17841250X-RAY DIFFRACTION100
4.8689-5.91470.25531480.21171280X-RAY DIFFRACTION100
5.9147-9.99310.25311430.22171301X-RAY DIFFRACTION100

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