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- PDB-6rcp: Crystal structure of the OmpK36 clinical isolate ST258 from Klebs... -

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Basic information

Entry
Database: PDB / ID: 6rcp
TitleCrystal structure of the OmpK36 clinical isolate ST258 from Klebsiella pneumonia
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / OmpK36 ST258
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transmembrane transport / cell outer membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.231 Å
AuthorsBeis, K. / Romano, M. / Kwong, J.
CitationJournal: Nat Commun / Year: 2019
Title: OmpK36-mediated Carbapenem resistance attenuates ST258 Klebsiella pneumoniae in vivo.
Authors: Wong, J.L.C. / Romano, M. / Kerry, L.E. / Kwong, H.S. / Low, W.W. / Brett, S.J. / Clements, A. / Beis, K. / Frankel, G.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OmpK36
B: OmpK36
E: OmpK36
G: OmpK36
H: OmpK36
I: OmpK36
K: OmpK36
L: OmpK36
N: OmpK36
O: OmpK36
P: OmpK36
Q: OmpK36
R: OmpK36
F: OmpK36
D: OmpK36
J: OmpK36
M: OmpK36
C: OmpK36


Theoretical massNumber of molelcules
Total (without water)688,97218
Polymers688,97218
Non-polymers00
Water00
1
A: OmpK36
B: OmpK36
F: OmpK36


Theoretical massNumber of molelcules
Total (without water)114,8293
Polymers114,8293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9550 Å2
ΔGint-52 kcal/mol
Surface area40090 Å2
MethodPISA
2
E: OmpK36
D: OmpK36
C: OmpK36


Theoretical massNumber of molelcules
Total (without water)114,8293
Polymers114,8293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-52 kcal/mol
Surface area39830 Å2
MethodPISA
3
G: OmpK36
H: OmpK36
I: OmpK36


Theoretical massNumber of molelcules
Total (without water)114,8293
Polymers114,8293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9870 Å2
ΔGint-54 kcal/mol
Surface area40060 Å2
MethodPISA
4
K: OmpK36
L: OmpK36
J: OmpK36


Theoretical massNumber of molelcules
Total (without water)114,8293
Polymers114,8293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9640 Å2
ΔGint-55 kcal/mol
Surface area40190 Å2
MethodPISA
5
N: OmpK36
O: OmpK36
M: OmpK36


Theoretical massNumber of molelcules
Total (without water)114,8293
Polymers114,8293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-51 kcal/mol
Surface area40180 Å2
MethodPISA
6
P: OmpK36
Q: OmpK36
R: OmpK36


Theoretical massNumber of molelcules
Total (without water)114,8293
Polymers114,8293
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-55 kcal/mol
Surface area40160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)286.035, 326.105, 164.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
OmpK36 / Outer membrane porin / Outer membrane protein C / Porin OmpC


Mass: 38276.199 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Details: ST258 mutant / Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ompK36, ompC, BANRA_01576, DXF97_01445, SAMEA3649709_00969
Production host: Escherichia coli (E. coli) / Strain (production host): Omp8 / References: UniProt: E5G6G2

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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: 5.56 Å3/Da / Density % sol: 77.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M LiSO4, 0.1 mM Tris HCl pH 8.5 and 30 % PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 3.23→286.03 Å / Num. obs: 127179 / % possible obs: 86.4 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.199 / Net I/σ(I): 6.6
Reflection shellResolution: 3.23→3.57 Å / Rmerge(I) obs: 1.11 / Num. unique obs: 6359 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5o79

5o79


Resolution: 3.231→91.514 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.59
RfactorNum. reflection% reflection
Rfree0.2499 6387 5.03 %
Rwork0.2181 --
obs0.2197 127092 51.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.231→91.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48762 0 0 0 48762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00349896
X-RAY DIFFRACTIONf_angle_d0.64867626
X-RAY DIFFRACTIONf_dihedral_angle_d4.14238754
X-RAY DIFFRACTIONf_chiral_restr0.0446930
X-RAY DIFFRACTIONf_plane_restr0.0049108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2313-3.2680.540640.326155X-RAY DIFFRACTION1
3.268-3.30640.258100.3556180X-RAY DIFFRACTION2
3.3064-3.34680.2962230.3117404X-RAY DIFFRACTION5
3.3468-3.38910.3767330.3179682X-RAY DIFFRACTION9
3.3891-3.43370.3301480.3033928X-RAY DIFFRACTION12
3.4337-3.48080.3522690.31811196X-RAY DIFFRACTION16
3.4808-3.53050.3508750.31251442X-RAY DIFFRACTION19
3.5305-3.58320.41371040.32051754X-RAY DIFFRACTION23
3.5832-3.63920.35171140.3222195X-RAY DIFFRACTION29
3.6392-3.69890.32441310.3052615X-RAY DIFFRACTION34
3.6989-3.76260.33461600.30932974X-RAY DIFFRACTION39
3.7626-3.83110.33671750.29453416X-RAY DIFFRACTION44
3.8311-3.90480.34652080.28883726X-RAY DIFFRACTION49
3.9048-3.98450.28132080.27344073X-RAY DIFFRACTION53
3.9845-4.07110.31142350.25214392X-RAY DIFFRACTION57
4.0711-4.16580.26332800.24434715X-RAY DIFFRACTION62
4.1658-4.270.26132540.22175069X-RAY DIFFRACTION66
4.27-4.38540.25472910.20765359X-RAY DIFFRACTION69
4.3854-4.51450.23633170.20165596X-RAY DIFFRACTION72
4.5145-4.66020.21993250.18935722X-RAY DIFFRACTION74
4.6602-4.82670.24423180.195909X-RAY DIFFRACTION76
4.8267-5.020.23363330.18496072X-RAY DIFFRACTION79
5.02-5.24840.2412980.19766257X-RAY DIFFRACTION80
5.2484-5.52510.23263310.19496312X-RAY DIFFRACTION81
5.5251-5.87120.24153280.2036453X-RAY DIFFRACTION83
5.8712-6.32440.25273210.2146655X-RAY DIFFRACTION85
6.3244-6.96070.23293420.19766662X-RAY DIFFRACTION85
6.9607-7.96740.21963680.19126576X-RAY DIFFRACTION84
7.9674-10.03610.2013490.18786668X-RAY DIFFRACTION84
10.0361-91.55040.22853350.23276648X-RAY DIFFRACTION81

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