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- PDB-5nhx: Periplasmic domain of Outer Membrane Protein A from Klebsiella pn... -

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Basic information

Entry
Database: PDB / ID: 5nhx
TitlePeriplasmic domain of Outer Membrane Protein A from Klebsiella pneumoniae
ComponentsOuter membrane protein A
KeywordsMEMBRANE PROTEIN / Outer membrane protein Klebsiella pneumoniae periplasmic domain
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
Similarity search - Function
Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain superfamily / OmpA family ...Outer membrane protein OmpA-like, transmembrane domain / Outer membrane protein, OmpA / OmpA-like transmembrane domain / Outer membrane protein, OmpA-like, conserved site / OmpA-like domain. / OmpA-like domain / Outer membrane protein, bacterial / : / OmpA-like domain superfamily / OmpA family / OmpA-like domain / OmpA-like domain profile. / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Outer membrane protein A
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDemange, P. / Tranier, S. / Nars, G. / Iordanov, I. / Mourey, L. / Saurel, O. / Milon, A.
CitationJournal: To Be Published
Title: Structure and dynamics of the C-terminal domain of OmpA from Klebsiella pneumonia
Authors: Nars, G. / Iordanov, I. / Saurel, O. / Tranier, S. / Mourey, L. / Milon, A. / Demange, P.
History
DepositionMar 22, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8392
Polymers13,6461
Non-polymers1921
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint1 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.650, 73.650, 61.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

21A-369-

HOH

31A-372-

HOH

41A-438-

HOH

51A-443-

HOH

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Components

#1: Protein Outer membrane protein A / Outer membrane protein II


Mass: 13646.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24017
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG6000 Citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97947 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.95→39.781 Å / Num. obs: 12873 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.714 % / Biso Wilson estimate: 27.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.066 / Χ2: 1.005 / Net I/σ(I): 21.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-27.7820.5873.969220.950.62998.6
2-2.067.7720.386.029030.970.407100
2.06-2.127.7610.3137.098740.9750.33699.8
2.12-2.188.0570.268.438600.9840.278100
2.18-2.257.5920.2159.088410.9840.231100
2.25-2.338.1790.17411.667950.990.18699.9
2.33-2.428.0950.14114.167860.9940.15100
2.42-2.528.0360.11317.187560.9950.121100
2.52-2.637.5940.09120.287340.9960.09899.9
2.63-2.767.9350.0823.246920.9960.085100
2.76-2.917.7380.06924.636610.9980.074100
2.91-3.087.8130.05928.986360.9980.064100
3.08-3.37.960.04637.415940.9990.04999.8
3.3-3.567.6610.0440.545630.9990.043100
3.56-3.97.2680.03941.295190.9990.042100
3.9-4.367.2140.03548.314770.9980.03799.8
4.36-5.047.3080.0350.784160.9990.03399.8
5.04-6.176.9860.03144.673690.9990.03399.5
6.17-8.736.6940.03147.192940.9990.033100
8.73-39.7815.9670.02451.0518110.02697.8

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Processing

Software
NameClassification
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ERH

4erh


Resolution: 1.95→39.781 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 17.45
RfactorNum. reflection% reflection
Rfree0.1939 1294 10.06 %
Rwork0.1765 --
obs0.1782 12866 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.95 Å2 / Biso mean: 33.3131 Å2 / Biso min: 15.41 Å2
Refinement stepCycle: final / Resolution: 1.95→39.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 0 13 148 1116
Biso mean--34.48 38.34 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061010
X-RAY DIFFRACTIONf_angle_d0.9081372
X-RAY DIFFRACTIONf_chiral_restr0.056154
X-RAY DIFFRACTIONf_plane_restr0.006184
X-RAY DIFFRACTIONf_dihedral_angle_d13.818396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.02810.26991530.22471223137699
2.0281-2.12040.22281430.195412631406100
2.1204-2.23220.18471500.192412611411100
2.2322-2.3720.19671170.19412851402100
2.372-2.55510.19181330.188612721405100
2.5551-2.81220.1931430.185812811424100
2.8122-3.2190.18941540.188712761430100
3.219-4.05490.18351440.161113131457100
4.0549-39.78920.19011570.15821398155599

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