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- PDB-4frt: Crystal Structure of Pseudomonas aeruginosa OccK7 (OpdD) -

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Basic information

Entry
Database: PDB / ID: 4frt
TitleCrystal Structure of Pseudomonas aeruginosa OccK7 (OpdD)
ComponentsProbable porin
KeywordsTRANSPORT PROTEIN / Beta-barrel / transporter (porin) / outer membrane
Function / homologyOuter membrane porin, bacterial / outer membrane porin, OprD family / Porin domain superfamily / porin activity / membrane / Probable porin
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.166 Å
AuthorsEren, E. / van den Berg, B.
CitationJournal: To be Published
Title: Crystal Structures of OccK Subfamily Proteins
Authors: Eren, E. / van den Berg, B.
History
DepositionJun 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_sheet_hbond ...pdbx_database_status / pdbx_struct_sheet_hbond / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _pdbx_database_status.pdb_format_compatible / _struct_ref_seq_dif.details
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable porin
B: Probable porin


Theoretical massNumber of molelcules
Total (without water)90,3382
Polymers90,3382
Non-polymers00
Water724
1
A: Probable porin


Theoretical massNumber of molelcules
Total (without water)45,1691
Polymers45,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable porin


Theoretical massNumber of molelcules
Total (without water)45,1691
Polymers45,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)152.250, 111.154, 99.933
Angle α, β, γ (deg.)90.00, 123.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable porin


Mass: 45169.043 Da / Num. of mol.: 2 / Fragment: unp residues 23-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA1025 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4U9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 400, 1M sodium formate, 0.05M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9764 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 1, 2012
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 3.2→40 Å / Num. obs: 23348 / % possible obs: 99.1 % / Redundancy: 7.7 % / Rsym value: 0.136 / Net I/σ(I): 18
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.55 / Rsym value: 0.889 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3T24

3t24


Resolution: 3.166→14.989 Å / SU ML: 0.35 / σ(F): 1.34 / Phase error: 29.55 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2687 1180 5.11 %
Rwork0.2096 --
obs0.2127 23088 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.166→14.989 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5912 0 0 4 5916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016039
X-RAY DIFFRACTIONf_angle_d1.3958151
X-RAY DIFFRACTIONf_dihedral_angle_d17.2632175
X-RAY DIFFRACTIONf_chiral_restr0.085847
X-RAY DIFFRACTIONf_plane_restr0.0061074
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1665-3.30910.30321580.21632498X-RAY DIFFRACTION90
3.3091-3.48150.28341260.22332749X-RAY DIFFRACTION98
3.4815-3.69660.30761150.22012753X-RAY DIFFRACTION98
3.6966-3.97710.30031620.22072751X-RAY DIFFRACTION99
3.9771-4.36830.28871720.21052753X-RAY DIFFRACTION99
4.3683-4.980.23631420.18622793X-RAY DIFFRACTION99
4.98-6.19950.25431440.22082785X-RAY DIFFRACTION100
6.1995-14.98880.25211610.20472826X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 29.5551 Å / Origin y: 3.8155 Å / Origin z: 24.2818 Å
111213212223313233
T0.2929 Å20.0086 Å2-0.027 Å2-0.3478 Å2-0.039 Å2--0.3311 Å2
L0.2684 °2-0.0187 °2-0.2549 °2-1.1672 °2-0.0329 °2--0.6569 °2
S0.0351 Å °0.0283 Å °-0.0267 Å °-0.1902 Å °-0.095 Å °0.1647 Å °-0.0602 Å °-0.0703 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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