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- PDB-4fms: Crystal structure of Pseudomonas aeruginosa OccK2 (OpdF) in compl... -

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Basic information

Entry
Database: PDB / ID: 4fms
TitleCrystal structure of Pseudomonas aeruginosa OccK2 (OpdF) in complex with glucuronate
ComponentsProbable porin
KeywordsTRANSPORT PROTEIN / Beta-barrel / Outer Membrane Transporter (Porin) / Glucuronate / 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
beta-D-glucopyranuronic acid / Chem-PGV / Probable porin
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
Authorsvan den Berg, B. / Eren, E.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Toward Understanding the Outer Membrane Uptake of Small Molecules by Pseudomonas aeruginosa.
Authors: Eren, E. / Parkin, J. / Adelanwa, A. / Cheneke, B. / Movileanu, L. / Khalid, S. / van den Berg, B.
History
DepositionJun 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Probable porin
A: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,44919
Polymers87,5352
Non-polymers5,91417
Water4,161231
1
B: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1289
Polymers43,7671
Non-polymers2,3618
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,32010
Polymers43,7671
Non-polymers3,5539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.435, 206.802, 51.747
Angle α, β, γ (deg.)90.00, 99.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Probable porin


Mass: 43767.457 Da / Num. of mol.: 2 / Fragment: unp residues 25-421
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA0240 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I6P8
#2: Sugar ChemComp-BDP / beta-D-glucopyranuronic acid / beta-D-glucuronic acid / D-glucuronic acid / glucuronic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H10O7
IdentifierTypeProgram
DGlcpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GlcpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcASNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 246 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.8 Å3/Da / Density % sol: 56.11 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 1K, 50 mM glucuronate, 50 mM Li2SO4, 50 mM Na2SO4 and 50 mM Na-acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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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 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 34356 / % possible obs: 89.5 %
Reflection shellResolution: 2.45→2.516 Å / % possible all: 90

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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 / Resolution: 2.45→14.992 Å / SU ML: 0.32 / σ(F): 1.38 / Phase error: 24.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 1888 5.85 %
Rwork0.1905 --
obs0.1936 32300 92.12 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.213 Å2 / ksol: 0.422 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0708 Å2-0 Å21.7615 Å2
2---5.1122 Å2-0 Å2
3---6.183 Å2
Refinement stepCycle: LAST / Resolution: 2.45→14.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5737 0 255 231 6223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086123
X-RAY DIFFRACTIONf_angle_d1.1748219
X-RAY DIFFRACTIONf_dihedral_angle_d19.3952288
X-RAY DIFFRACTIONf_chiral_restr0.077828
X-RAY DIFFRACTIONf_plane_restr0.0041057
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.5160.27751410.19342232X-RAY DIFFRACTION90
2.516-2.58960.29591420.19732233X-RAY DIFFRACTION86
2.5896-2.67280.24381410.18782218X-RAY DIFFRACTION88
2.6728-2.76770.27111360.19362247X-RAY DIFFRACTION89
2.7677-2.87780.30991350.20212229X-RAY DIFFRACTION87
2.8778-3.00780.2811410.19642266X-RAY DIFFRACTION90
3.0078-3.16490.26261420.19372297X-RAY DIFFRACTION91
3.1649-3.36120.25241520.19252403X-RAY DIFFRACTION94
3.3612-3.61730.22811460.18432457X-RAY DIFFRACTION97
3.6173-3.97520.23951510.19052481X-RAY DIFFRACTION97
3.9752-4.53640.18461550.17252447X-RAY DIFFRACTION97
4.5364-5.66360.21731540.17142468X-RAY DIFFRACTION97
5.6636-14.99220.27231520.23042434X-RAY DIFFRACTION95

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