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- PDB-8pyz: Structure of Ompk36GD from Klebsiella pneumonia, solved at wavele... -

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Basic information

Entry
Database: PDB / ID: 8pyz
TitleStructure of Ompk36GD from Klebsiella pneumonia, solved at wavelength 4.13 A
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / carbapenemase
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 domain superfamily
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsDuman, R. / El Omari, K. / Mykhaylyk, V. / Orr, C. / Kwong, H. / Beis, K. / Wagner, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: OmpK36
F: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,22012
Polymers114,6933
Non-polymers2,5279
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13040 Å2
ΔGint-51 kcal/mol
Surface area40040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.033, 74.366, 90.119
Angle α, β, γ (deg.)90.000, 112.039, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPHEPHE(chain 'C' and (resid 1 through 141 or resid 145...CC1 - 1411 - 141
12ASPASPPHEPHE(chain 'C' and (resid 1 through 141 or resid 145...CC145 - 347145 - 347
13LDALDALDALDA(chain 'C' and (resid 1 through 141 or resid 145...CK402
21GLYGLYPHEPHE(chain 'E' and (resid 1 through 347 or resid 401))EA1 - 1411 - 141
22ASPASPPHEPHE(chain 'E' and (resid 1 through 347 or resid 401))EA145 - 347145 - 347
23LDALDALDALDA(chain 'E' and (resid 1 through 347 or resid 401))CJ401
31GLYGLYPHEPHE(chain 'F' and (resid 1 through 141 or resid 145 through 347 or resid 401))FB1 - 1411 - 141
32ASPASPPHEPHE(chain 'F' and (resid 1 through 141 or resid 145 through 347 or resid 401))FB145 - 347145 - 347
33LDALDALDALDA(chain 'F' and (resid 1 through 141 or resid 145 through 347 or resid 401))EG504

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Components

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


Mass: 38231.062 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36, ompC_2, DDJ63_09115, NCTC13443_05288 / Production host: Escherichia coli (E. coli) / References: UniProt: D6QLY1
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 4.1328 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Oct 7, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 4.1328 Å / Relative weight: 1
ReflectionResolution: 2.7→83.53 Å / Num. obs: 77000 / % possible obs: 97.4 % / Redundancy: 22.3 % / Biso Wilson estimate: 48.86 Å2 / CC1/2: 0.996 / Net I/σ(I): 24.03
Reflection shellResolution: 2.702→2.799 Å / Num. unique obs: 3499 / CC1/2: 0.957

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→83.53 Å / SU ML: 0.3544 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.4222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2408 3792 5.16 %
Rwork0.1979 69705 -
obs0.2001 73497 95.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.92 Å2
Refinement stepCycle: LAST / Resolution: 2.7→83.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8099 0 97 82 8278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228366
X-RAY DIFFRACTIONf_angle_d0.527511297
X-RAY DIFFRACTIONf_chiral_restr0.03951130
X-RAY DIFFRACTIONf_plane_restr0.00231508
X-RAY DIFFRACTIONf_dihedral_angle_d15.52442943
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.730.28741140.25952092X-RAY DIFFRACTION76.25
2.73-2.770.32181460.27292402X-RAY DIFFRACTION90.26
2.77-2.810.32321310.26312532X-RAY DIFFRACTION93.18
2.81-2.850.30211410.25632498X-RAY DIFFRACTION91.31
2.85-2.890.30381240.25872454X-RAY DIFFRACTION91.81
2.89-2.940.30151300.23822531X-RAY DIFFRACTION93.3
2.94-2.980.36111410.24432557X-RAY DIFFRACTION93.13
2.98-3.040.33991360.23832473X-RAY DIFFRACTION94.36
3.04-3.090.25331440.22432583X-RAY DIFFRACTION92.69
3.09-3.150.29421360.22822523X-RAY DIFFRACTION95.3
3.15-3.210.24681370.22872605X-RAY DIFFRACTION94.81
3.21-3.280.2921460.22122527X-RAY DIFFRACTION95.26
3.28-3.360.23941440.21582615X-RAY DIFFRACTION95.4
3.36-3.440.27831450.19852608X-RAY DIFFRACTION96.43
3.44-3.540.25141440.19872616X-RAY DIFFRACTION96.03
3.54-3.640.22911410.20662579X-RAY DIFFRACTION96.66
3.64-3.760.24881490.19952645X-RAY DIFFRACTION97.49
3.76-3.890.27231350.20512667X-RAY DIFFRACTION98.56
3.89-4.050.22651440.1962646X-RAY DIFFRACTION98.1
4.05-4.230.20661480.16872694X-RAY DIFFRACTION99.06
4.23-4.460.22791430.16072660X-RAY DIFFRACTION98.8
4.46-4.740.17681460.14772705X-RAY DIFFRACTION99.2
4.74-5.10.19921520.16312697X-RAY DIFFRACTION99.86
5.1-5.620.19031470.15732695X-RAY DIFFRACTION99.89
5.62-6.430.25761390.18932715X-RAY DIFFRACTION99.93
6.43-8.10.21131420.19832699X-RAY DIFFRACTION99.79
8.1-83.530.22211470.21422687X-RAY DIFFRACTION99.23
Refinement TLS params.Method: refined / Origin x: 9.08985191577 Å / Origin y: 36.6112731869 Å / Origin z: 52.9366931275 Å
111213212223313233
T0.377383809735 Å2-0.00224262906157 Å2-0.0725013787636 Å2-0.436213163058 Å20.00498577179559 Å2--0.576723066291 Å2
L0.334553795137 °2-0.0541374440603 °2-0.10718530445 °2-0.390220341698 °20.0203281979024 °2--0.305582078965 °2
S0.0078891094528 Å °-0.0292624323331 Å °-0.0329383677024 Å °0.021691303439 Å °-0.0156011835871 Å °-0.0481565657225 Å °0.0209785411725 Å °0.0503602188461 Å °0.0095894972143 Å °
Refinement TLS groupSelection details: all

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