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- PDB-5u1h: Crystal structure of the C-terminal peptidoglycan binding domain ... -

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Basic information

Entry
Database: PDB / ID: 5u1h
TitleCrystal structure of the C-terminal peptidoglycan binding domain of OprF (PA1777) from Pseudomonas aeruginosa
ComponentsOuter membrane porin F
KeywordsPEPTIDE BINDING PROTEIN / peptidoglycan binding protein / OprF / OmpA / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


adhesion of symbiont to host / complement component C3b binding / outer membrane / porin activity / pore complex / monoatomic ion transport / cell outer membrane / regulation of cell shape / calcium ion binding
Similarity search - Function
Outer membrane porin F, N-terminal / OprF membrane domain / TSP type-3 repeat / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily ...Outer membrane porin F, N-terminal / OprF membrane domain / TSP type-3 repeat / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain profile. / OmpA-like domain superfamily / OmpA family / OmpA-like domain / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-7QA / ACETATE ION / Outer membrane porin F
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWatanabe, N. / Stogios, P.J. / Skarina, T. / Wawrzak, Z. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be published
Title: Crystal structure of the C-terminal peptidoglycan binding domain of OprF (PA1777) from Pseudomonas aeruginosa
Authors: Watanabe, N.
History
DepositionNov 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Outer membrane porin F
B: Outer membrane porin F
C: Outer membrane porin F
D: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,28124
Polymers53,7794
Non-polymers2,50220
Water13,727762
1
A: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8444
Polymers13,4451
Non-polymers4003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3259
Polymers13,4451
Non-polymers8808
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1346
Polymers13,4451
Non-polymers6905
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Outer membrane porin F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9785
Polymers13,4451
Non-polymers5334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11410 Å2
ΔGint-172 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.340, 55.920, 79.080
Angle α, β, γ (deg.)90.000, 107.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Outer membrane porin F


Mass: 13444.705 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: oprF, PA1777 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P13794

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Non-polymers , 5 types, 782 molecules

#2: Chemical
ChemComp-7QA / (2R,6S)-2-amino-6-(carboxyamino)-7-{[(1R)-1-carboxyethyl]amino}-7-oxoheptanoic acid


Mass: 305.284 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H19N3O7
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 4 / Details: ammonium sulphate 2.5M, Na Acetate 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→31.23 Å / Num. obs: 69727 / % possible obs: 98.2 % / Redundancy: 5 % / Biso Wilson estimate: 13.81 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.039 / Rrim(I) all: 0.09 / Net I/σ(I): 11.6 / Num. measured all: 346742 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.544.10.6052074450070.7180.3280.6922.395.5
6.71-31.234.50.05537868340.9950.0280.06223.998.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.28data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TD4

3td4


Resolution: 1.5→31.232 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1973 2.88 %
Rwork0.1664 66591 -
obs0.1674 68564 96.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.11 Å2 / Biso mean: 19.5852 Å2 / Biso min: 6.92 Å2
Refinement stepCycle: final / Resolution: 1.5→31.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 150 762 4670
Biso mean--34.73 29.54 -
Num. residues----490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.023985
X-RAY DIFFRACTIONf_angle_d0.9285402
X-RAY DIFFRACTIONf_chiral_restr0.08605
X-RAY DIFFRACTIONf_plane_restr0.004727
X-RAY DIFFRACTIONf_dihedral_angle_d19.8871462
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53750.261250.25854338446388
1.5375-1.57910.25831330.23544510464392
1.5791-1.62560.26381380.21724602474094
1.6256-1.6780.27361390.20734668480795
1.678-1.7380.23261420.19094675481796
1.738-1.80760.21351430.18154729487296
1.8076-1.88980.1981450.16794756490197
1.8898-1.98950.22331450.17274822496798
1.9895-2.11410.21421380.16724824496298
2.1141-2.27730.24111500.16284857500799
2.2773-2.50630.1661430.16864898504199
2.5063-2.86880.1981450.16714914505999
2.8688-3.61350.17341410.14294948508999
3.6135-31.23860.16411460.144150505196100

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