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- PDB-4frx: Crystal Structure of Pseudomonas aeruginosa OccK8 (OprE) -

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Basic information

Entry
Database: PDB / ID: 4frx
TitleCrystal Structure of Pseudomonas aeruginosa OccK8 (OprE)
ComponentsAnaerobically-induced outer membrane porin OprE
KeywordsTRANSPORT PROTEIN / beta-barrel / transporter (porin) / outer membrane
Function / homology
Function and homology information


outer membrane / porin activity
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
Anaerobically-induced outer membrane porin OprE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Sep 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: Anaerobically-induced outer membrane porin OprE
B: Anaerobically-induced outer membrane porin OprE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,91611
Polymers95,1582
Non-polymers2,7589
Water10,341574
1
A: Anaerobically-induced outer membrane porin OprE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1116
Polymers47,5791
Non-polymers1,5325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anaerobically-induced outer membrane porin OprE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8055
Polymers47,5791
Non-polymers1,2264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.386, 90.121, 103.598
Angle α, β, γ (deg.)90.00, 92.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-643-

HOH

21B-655-

HOH

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Components

#1: Protein Anaerobically-induced outer membrane porin OprE


Mass: 47579.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: oprE, PA0291 / Production host: Escherichia coli (E. coli) / References: UniProt: G3XDA5
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 574 / 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: 3.39 Å3/Da / Density % sol: 63.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% PEG 400, 0.2M ammonium sulphate, 0.05M HEPES, pH 7.0, 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
RadiationMonochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 99602 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rsym value: 0.118 / Net I/σ(I): 9.2
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.93 / Num. unique all: 4913 / Rsym value: 0.553 / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SYS

3sys


Resolution: 1.9→14.993 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 22.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2469 1994 2.01 %
Rwork0.2133 --
obs0.214 99141 99.26 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.336 Å2 / ksol: 0.44 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1631 Å20 Å2-0.6708 Å2
2---1.1716 Å2-0 Å2
3---3.3347 Å2
Refinement stepCycle: LAST / Resolution: 1.9→14.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6105 0 114 574 6793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076387
X-RAY DIFFRACTIONf_angle_d1.1378605
X-RAY DIFFRACTIONf_dihedral_angle_d15.4552261
X-RAY DIFFRACTIONf_chiral_restr0.084906
X-RAY DIFFRACTIONf_plane_restr0.0051121
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94740.25051410.21866841X-RAY DIFFRACTION99
1.9474-20.25061330.2096904X-RAY DIFFRACTION99
2-2.05870.26011400.20816853X-RAY DIFFRACTION99
2.0587-2.12490.25041380.20186891X-RAY DIFFRACTION99
2.1249-2.20070.23831500.19846857X-RAY DIFFRACTION99
2.2007-2.28850.25471330.20276945X-RAY DIFFRACTION99
2.2885-2.39220.24981400.20986854X-RAY DIFFRACTION99
2.3922-2.51780.2781530.20596929X-RAY DIFFRACTION99
2.5178-2.67470.23461400.21916969X-RAY DIFFRACTION100
2.6747-2.87990.2431390.20886979X-RAY DIFFRACTION100
2.8799-3.16720.25281460.21796979X-RAY DIFFRACTION100
3.1672-3.61990.21421490.20157024X-RAY DIFFRACTION100
3.6199-4.53960.24761420.20917019X-RAY DIFFRACTION100
4.5396-14.99310.25941500.24927103X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.2622 Å / Origin y: -6.8936 Å / Origin z: 74.2133 Å
111213212223313233
T0.0218 Å2-0.0204 Å20.0002 Å2-0.0233 Å2-0.0001 Å2--0.0269 Å2
L0.0093 °20.0109 °2-0.0027 °2-0.0231 °20.0192 °2--0.0183 °2
S-0.0169 Å °0.0054 Å °-0.0008 Å °-0.0029 Å °-0.002 Å °0.0011 Å °-0.0026 Å °0.0065 Å °-0.0199 Å °
Refinement TLS groupSelection details: all

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