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- PDB-6rd3: Crystal structure of the wild type OmpK36 from Klebsiella pneumonia -

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Basic information

Entry
Database: PDB / ID: 6rd3
TitleCrystal structure of the wild type OmpK36 from Klebsiella pneumonia
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / OmpK36 WT
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: 1.98 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 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OmpK36
B: OmpK36
C: OmpK36
D: OmpK36
E: OmpK36
F: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,38641
Polymers228,3546
Non-polymers9,03335
Water15,889882
1
A: OmpK36
B: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,45923
Polymers114,1773
Non-polymers5,28220
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15840 Å2
ΔGint-42 kcal/mol
Surface area39410 Å2
MethodPISA
2
D: OmpK36
E: OmpK36
F: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,92718
Polymers114,1773
Non-polymers3,75015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12970 Å2
ΔGint-56 kcal/mol
Surface area40230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.090, 316.090, 73.790
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
OmpK36


Mass: 38058.918 Da / Num. of mol.: 6 / Mutation: G0
Source method: isolated from a genetically manipulated source
Details: G0 is from cloning / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36 / Production host: Escherichia coli (E. coli) / Variant (production host): omp8 / References: UniProt: D6QLY0
#2: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Lithium sulfate, 0.1M sodium citrate pH 5.6 and 12% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→53.2 Å / Num. obs: 169857 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.023 / Net I/σ(I): 6.3
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 0.134 / Num. unique obs: 8440 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5O79

5o79


Resolution: 1.98→53.197 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 8540 5.03 %
Rwork0.1937 --
obs0.1957 169757 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→53.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16114 0 287 882 17283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00616720
X-RAY DIFFRACTIONf_angle_d0.83422525
X-RAY DIFFRACTIONf_dihedral_angle_d7.9719532
X-RAY DIFFRACTIONf_chiral_restr0.0522256
X-RAY DIFFRACTIONf_plane_restr0.0043000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00250.35042600.28275402X-RAY DIFFRACTION100
2.0025-2.02610.30982840.25615359X-RAY DIFFRACTION100
2.0261-2.05080.30572900.2545429X-RAY DIFFRACTION100
2.0508-2.07670.28922840.24365274X-RAY DIFFRACTION100
2.0767-2.10410.27852770.22935424X-RAY DIFFRACTION100
2.1041-2.13290.28463140.22965295X-RAY DIFFRACTION100
2.1329-2.16340.26282790.22095383X-RAY DIFFRACTION100
2.1634-2.19570.26343050.21065372X-RAY DIFFRACTION100
2.1957-2.230.26332970.20985348X-RAY DIFFRACTION100
2.23-2.26650.25772870.2075376X-RAY DIFFRACTION100
2.2665-2.30560.23333230.20025389X-RAY DIFFRACTION100
2.3056-2.34750.22982770.19355276X-RAY DIFFRACTION100
2.3475-2.39270.27822830.2035427X-RAY DIFFRACTION100
2.3927-2.44150.24972870.2045302X-RAY DIFFRACTION100
2.4415-2.49460.27343010.20595393X-RAY DIFFRACTION100
2.4946-2.55260.26562570.20375414X-RAY DIFFRACTION100
2.5526-2.61650.24322650.18985394X-RAY DIFFRACTION100
2.6165-2.68720.24042760.18795297X-RAY DIFFRACTION100
2.6872-2.76630.24142940.19325426X-RAY DIFFRACTION100
2.7663-2.85560.23833090.19175336X-RAY DIFFRACTION100
2.8556-2.95760.23562830.18275388X-RAY DIFFRACTION100
2.9576-3.0760.22422790.17725409X-RAY DIFFRACTION100
3.076-3.2160.20772870.16935354X-RAY DIFFRACTION100
3.216-3.38550.21792710.17275395X-RAY DIFFRACTION100
3.3855-3.59760.19492800.17345338X-RAY DIFFRACTION100
3.5976-3.87530.23042560.1815439X-RAY DIFFRACTION100
3.8753-4.26510.20762790.18335405X-RAY DIFFRACTION100
4.2651-4.8820.19533030.16685354X-RAY DIFFRACTION100
4.882-6.14930.19992730.19465429X-RAY DIFFRACTION100
6.1493-53.21610.23342800.20555390X-RAY DIFFRACTION100

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