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- PDB-1osm: OSMOPORIN (OMPK36) FROM KLEBSIELLA PNEUMONIAE -

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Basic information

Entry
Database: PDB / ID: 1osm
TitleOSMOPORIN (OMPK36) FROM KLEBSIELLA PNEUMONIAE
ComponentsOMPK36
KeywordsOUTER MEMBRANE PROTEIN / NON-SPECIFIC PORIN / OSMOPORIN / BETA-BARREL / TRANSMEMBRANE
Function / homology
Function and homology information


porin activity / pore complex / cell outer membrane / monoatomic ion transmembrane transport
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
DODECANE / Outer membrane porin C
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsDutzler, R. / Schirmer, T.
CitationJournal: Structure Fold.Des. / Year: 1999
Title: Crystal structure and functional characterization of OmpK36, the osmoporin of Klebsiella pneumoniae.
Authors: Dutzler, R. / Rummel, G. / Alberti, S. / Hernandez-Alles, S. / Phale, P. / Rosenbusch, J. / Benedi, V. / Schirmer, T.
History
DepositionJan 8, 1999Processing site: BNL
Revision 1.0Jul 26, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Other
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)114,42412
Polymers112,8913
Non-polymers1,5339
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11730 Å2
ΔGint-37 kcal/mol
Surface area43510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.800, 76.800, 223.400
Angle α, β, γ (deg.)90.00, 113.30, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.3107, -0.81168, -0.49462), (0.80794, -0.49964, 0.31239), (-0.50069, -0.30256, 0.81103)0.21986, -0.24846, 0.0397
3given(-0.31118, 0.80736, -0.50134), (-0.81382, -0.49881, -0.29814), (-0.49077, 0.31522, 0.81227)0.43057, -0.0653, 0.11301

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Components

#1: Protein OMPK36 / OSMOPORIN


Mass: 37630.477 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q48473
#2: Chemical
ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C12H26
Sequence detailsTHE RESIDUE NUMBERING IS BASED ON THE HOMOLOGOUS MATRIX PORIN FROM E.COLI (OMPF, PDB CODE 2OMF). ...THE RESIDUE NUMBERING IS BASED ON THE HOMOLOGOUS MATRIX PORIN FROM E.COLI (OMPF, PDB CODE 2OMF). CONSEQUENTLY, THERE ARE GAPS IN THE NUMBERING (27-31,75-76,243-247) AND INSERTIONS (163A-J,181A AND 322A-C).

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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: 3.3 Å3/Da
Crystal growpH: 9.8 / Details: pH 9.8
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.6 %C8HESO11
20.1 %octyl-POE11
30.5 M11MgCl2
40.05 MTris-HCl11
515 %PEG200011

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.94
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 47412 / % possible obs: 96.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 3.7
Reflection shellResolution: 3.2→3.31 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 97.2
Reflection shell
*PLUS
% possible obs: 97.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OMF

2omf


Resolution: 3.2→15 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: STRICT NCS COORDINATE AND B-FACTOR CONSTRAINTS USED FOR THE 6 PROTEIN CHAINS IN THE ASYMMETRIC UNITS. THE TWO GROUPS OF DETERGENTS (MODELED AS 2X9 DODECANE MOLECULES) WERE REFINED WITH 2- ...Details: STRICT NCS COORDINATE AND B-FACTOR CONSTRAINTS USED FOR THE 6 PROTEIN CHAINS IN THE ASYMMETRIC UNITS. THE TWO GROUPS OF DETERGENTS (MODELED AS 2X9 DODECANE MOLECULES) WERE REFINED WITH 2-FOLD STRICT NCS CONSTRAINTS. ONE GROUP B-FACTOR PER DETERGENT MOLECULE.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 -10 %RANDOM
Rwork0.208 ---
obs0.208 47412 96.1 %-
Displacement parametersBiso mean: 55.3 Å2
Refine analyzeLuzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7992 0 108 0 8100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT NCS CONSTRAINTS
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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