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- PDB-5o79: Klebsiella pneumoniae OmpK36 -

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Basic information

Entry
Database: PDB / ID: 5o79
TitleKlebsiella pneumoniae OmpK36
ComponentsOmpK36
KeywordsMEMBRANE PROTEIN / Outer membrane protein / porin / ion transport / OmpC ortholog
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: 1.65 Å
Authorsvan den berg, B. / Pathania, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Union United Kingdom
CitationJournal: Acs Infect Dis. / Year: 2018
Title: Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins.
Authors: Acosta-Gutierrez, S. / Ferrara, L. / Pathania, M. / Masi, M. / Wang, J. / Bodrenko, I. / Zahn, M. / Winterhalter, M. / Stavenger, R.A. / Pages, J.M. / Naismith, J.H. / van den Berg, B. / ...Authors: Acosta-Gutierrez, S. / Ferrara, L. / Pathania, M. / Masi, M. / Wang, J. / Bodrenko, I. / Zahn, M. / Winterhalter, M. / Stavenger, R.A. / Pages, J.M. / Naismith, J.H. / van den Berg, B. / Page, M.G.P. / Ceccarelli, M.
History
DepositionJun 8, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 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 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

Downloads & links

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Assembly

Deposited unit
A: OmpK36
B: OmpK36
C: OmpK36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,92415
Polymers114,0933
Non-polymers2,83112
Water11,440635
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12570 Å2
ΔGint-68 kcal/mol
Surface area39550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.316, 74.511, 90.814
Angle α, β, γ (deg.)90.00, 112.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein OmpK36


Mass: 38030.934 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ompK36 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Omp8 / References: UniProt: D6QLY0
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 3.37 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.08 M Magnesium Acetate tetrahydrate , 0.1 M sodium citrate, 14% w/v 5000 PEG MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→107.57 Å / Num. obs: 169933 / % possible obs: 98.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 16.98 Å2 / Rpim(I) all: 0.039 / Net I/σ(I): 11.6
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 8276 / CC1/2: 0.689 / Rpim(I) all: 0.607 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OSM

1osm


Resolution: 1.65→107.57 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.242 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18963 8563 5 %RANDOM
Rwork0.14611 ---
obs0.14829 161366 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.285 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å2-0 Å20.65 Å2
2---0.52 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 1.65→107.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8027 0 57 635 8719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.028252
X-RAY DIFFRACTIONr_bond_other_d0.0030.027483
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.92811148
X-RAY DIFFRACTIONr_angle_other_deg0.939316821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.36151024
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94124.88459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56151231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7111539
X-RAY DIFFRACTIONr_chiral_restr0.1070.21126
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029915
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022148
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0642.6024105
X-RAY DIFFRACTIONr_mcbond_other3.0652.6024104
X-RAY DIFFRACTIONr_mcangle_it3.7453.9155123
X-RAY DIFFRACTIONr_mcangle_other3.7453.9155124
X-RAY DIFFRACTIONr_scbond_it4.1843.0634146
X-RAY DIFFRACTIONr_scbond_other4.1853.0634147
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7894.4426025
X-RAY DIFFRACTIONr_long_range_B_refined5.17722.9569461
X-RAY DIFFRACTIONr_long_range_B_other4.94522.6629253
X-RAY DIFFRACTIONr_rigid_bond_restr2.785315729
X-RAY DIFFRACTIONr_sphericity_free35.7425272
X-RAY DIFFRACTIONr_sphericity_bonded15.522515930
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 615 -
Rwork0.272 11734 -
obs--97.2 %

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