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- PDB-4ft6: Crystal Structure of Pseudomonas aeruginosa OccK9 (OpdG) -

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Basic information

Entry
Database: PDB / ID: 4ft6
TitleCrystal Structure of Pseudomonas aeruginosa OccK9 (OpdG)
ComponentsProbable porin
KeywordsTRANSPORT PROTEIN / Beta-barrel / Transporter (porin) / 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
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 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 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3246
Polymers43,6161
Non-polymers1,7085
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.479, 96.479, 148.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-533-

HOH

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Components

#1: Protein Probable porin


Mass: 43615.656 Da / Num. of mol.: 1 / Fragment: unp residues 29-416
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA2213 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I1Q4
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 4.56 Å3/Da / Density % sol: 73.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% PEG 1000, 0.2M potassium fluoride, 0.05M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 25080 / % possible obs: 100 % / Redundancy: 9.2 % / Rsym value: 0.07 / Net I/σ(I): 31
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.75 / Rsym value: 0.773 / % possible all: 100

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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 3SYS

3sys


Resolution: 2.603→14.93 Å / SU ML: 0.25 / σ(F): 1.35 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2399 1268 5.1 %
Rwork0.2039 --
obs0.2058 24876 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.603→14.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 82 37 3073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083092
X-RAY DIFFRACTIONf_angle_d1.2084159
X-RAY DIFFRACTIONf_dihedral_angle_d18.0971183
X-RAY DIFFRACTIONf_chiral_restr0.081430
X-RAY DIFFRACTIONf_plane_restr0.005543
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6027-2.70630.31311390.25662539X-RAY DIFFRACTION99
2.7063-2.82870.24231330.22222620X-RAY DIFFRACTION100
2.8287-2.97670.25611370.21562570X-RAY DIFFRACTION100
2.9767-3.16150.27521420.21992610X-RAY DIFFRACTION100
3.1615-3.4030.27811440.21882604X-RAY DIFFRACTION100
3.403-3.74050.24491430.20442610X-RAY DIFFRACTION100
3.7405-4.27070.22151570.20332609X-RAY DIFFRACTION100
4.2707-5.33940.20051400.17892669X-RAY DIFFRACTION100
5.3394-14.93050.25541330.20622777X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -56.4955 Å / Origin y: 13.4301 Å / Origin z: -32.9872 Å
111213212223313233
T0.515 Å20.0666 Å20.0071 Å2-0.2695 Å2-0.0265 Å2--0.5539 Å2
L1.7887 °2-0.2847 °2-0.3268 °2-1.9319 °2-0.1135 °2--1.3651 °2
S-0.0977 Å °-0.0766 Å °-0.0126 Å °0.0434 Å °0.1908 Å °-0.054 Å °-0.1469 Å °-0.0932 Å °-0.093 Å °
Refinement TLS groupSelection details: all

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