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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 / homologyOuter membrane porin, bacterial / Porin domain superfamily / outer membrane porin, OprD family / go:0022838: / integral component of cell outer membrane / porin activity / Probable porin
Function and homology information
Specimen sourcePseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.45 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 18, 2012 / Release: Mar 13, 2013
RevisionDateData content typeGroupProviderType
1.0Mar 13, 2013Structure modelrepositoryInitial release
1.1Mar 27, 2013Structure modelDatabase references
1.2May 22, 2013Structure modelDatabase references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,44919
Polyers87,5352
Non-polymers5,91417
Water4,161231
1
B: Probable porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1289
Polyers43,7671
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
Polyers43,7671
Non-polymers3,5539
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
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-MP 1 21 1

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Components

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Protein/peptide , 1 types, 2 molecules BA

#1: Protein/peptide Probable porin


Mass: 43767.457 Da / Num. of mol.: 2 / Fragment: unp residues 25-421 / 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

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Non-polymers , 5 types, 248 molecules

#2: Chemical ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 2 / Formula: C6H10O7 / Glucuronic acid
#3: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 306.438 Da / Num. of mol.: 7 / 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 / Formula: C40H77O10P / Phosphatidylglycerol / Comment: phospholipid *YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Formula: H2O / Water

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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 / Density percent 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 kelvins
SourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Collection date: Feb 1, 2011
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionD resolution high: 2.45 Å / D resolution low: 50 Å / Number obs: 34356 / Percent possible obs: 89.5
Reflection shellHighest resolution: 2.45 Å / Lowest resolution: 2.516 Å / Percent 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
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.32 / Sigma F: 1.38 / Overall phase error: 24.52 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.73 Å / Solvent vdw probe radii: 1 Å / Solvent model details: FLAT BULK SOLVENT MODEL / Solvent model param bsol: 60.213 / Solvent model param ksol: 0.422
Displacement parametersAniso B11: -1.0708 Å2 / Aniso B12: - Å2 / Aniso B13: 1.7615 Å2 / Aniso B22: -5.1122 Å2 / Aniso B23: - Å2 / Aniso B33: 6.183 Å2
Least-squares processR factor R free: 0.2425 / R factor R work: 0.1905 / R factor obs: 0.1936 / Highest resolution: 2.45 Å / Lowest resolution: 14.992 Å / Number reflection R free: 1888 / Number reflection obs: 32300 / Percent reflection R free: 5.85 / Percent reflection obs: 92.12
Refine hist #LASTHighest resolution: 2.45 Å / Lowest resolution: 14.992 Å
Number of atoms included #LASTProtein: 5737 / Nucleic acid: 0 / Ligand: 255 / Solvent: 231 / Total: 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
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.45000.27750.19342.5160141223290.00
2.51600.29590.19732.5896142223386.00
2.58960.24380.18782.6728141221888.00
2.67280.27110.19362.7677136224789.00
2.76770.30990.20212.8778135222987.00
2.87780.28100.19643.0078141226690.00
3.00780.26260.19373.1649142229791.00
3.16490.25240.19253.3612152240394.00
3.36120.22810.18433.6173146245797.00
3.61730.23950.19053.9752151248197.00
3.97520.18460.17254.5364155244797.00
4.53640.21730.17145.6636154246897.00
5.66360.27230.230414.9922152243495.00

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