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- PDB-2omf: OMPF PORIN -

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Basic information

Entry
Database: PDB / ID: 2omf
TitleOMPF PORIN
ComponentsMATRIX PORIN OUTER MEMBRANE PROTEIN F
KeywordsINTEGRAL MEMBRANE PROTEIN PORIN / PORIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity ...colicin transmembrane transporter activity / monoatomic ion channel complex / porin activity / pore complex / protein homotrimerization / monoatomic ion transmembrane transport / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / monoatomic ion channel activity / lipid binding / membrane / identical protein binding
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Porin domain, Gram-negative type / Gram-negative porin / Porin, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin F
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsCowan, S.W.
Citation
Journal: To be Published
Title: The Refined Structure of Ompf Porin from E.Coli at 2.4 Angstroms Resolution
Authors: Cowan, S.W.
#1: Journal: Nature / Year: 1992
Title: Crystal Structures Explain Functional Properties of Two E.Coli Porins
Authors: Cowan, S.W. / Schirmer, T. / Rummel, G. / Steiert, M. / Ghosh, R. / Pauptit, R.A. / Jansonius, J.N. / Rosenbusch, J.P.
#2: Journal: J.Mol.Biol. / Year: 1991
Title: Trigonal Crystals of Porin from Escherichia Coli
Authors: Pauptit, R.A. / Zhang, H. / Rummel, G. / Schirmer, T. / Jansonius, J.N. / Rosenbusch, J.P.
History
DepositionFeb 28, 1995Processing site: BNL
SupersessionDec 7, 1995ID: 1OMF
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATRIX PORIN OUTER MEMBRANE PROTEIN F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,79213
Polymers37,1141
Non-polymers3,67712
Water2,306128
1
A: MATRIX PORIN OUTER MEMBRANE PROTEIN F
hetero molecules

A: MATRIX PORIN OUTER MEMBRANE PROTEIN F
hetero molecules

A: MATRIX PORIN OUTER MEMBRANE PROTEIN F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,37539
Polymers111,3433
Non-polymers11,03236
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13180 Å2
ΔGint19 kcal/mol
Surface area45570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.500, 118.500, 52.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsSYMMETRY THE CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS PRESENTED BELOW GENERATE THE SUBUNITS OF THE POLYMERIC MOLECULE. APPLIED TO RESIDUES: 1 .. 340 1ST SUBUNIT TO 2ND SUBUNIT IN TRIMER SYMMETRY1 1 -0.500000 0.865979 0.000000 -59.25000 SYMMETRY2 1 -0.866071 -0.500000 0.000000 102.63000 SYMMETRY3 1 0.000000 0.000000 1.000000 0.00000 APPLIED TO RESIDUES: 1 .. 340 1ST SUBUNIT TO THIRD SUBUNIT IN TRIMER SYMMETRY1 2 -0.500000 -0.865979 0.000000 59.25000 SYMMETRY2 2 0.866071 -0.500000 0.000000 102.63000 SYMMETRY3 2 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein MATRIX PORIN OUTER MEMBRANE PROTEIN F / MATRIX PORIN / OMPF PORIN


Mass: 37114.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / References: UniProt: P02931
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.88 Å3/Da / Density % sol: 57.26 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.009 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 11, 1991
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionNum. obs: 16989 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.077

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.4→8 Å / σ(F): 0
Details: ASN 27 COULD NOT BE MODELED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND IS INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION (WITH OCCUPANCIES SET TO ZERO). THE HET RESIDUES 341 - 354 ...Details: ASN 27 COULD NOT BE MODELED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND IS INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION (WITH OCCUPANCIES SET TO ZERO). THE HET RESIDUES 341 - 354 HAVE NOT BEEN IDENTIFIED UNAMBIGUOUSLY AND HAVE BEEN MODELED AS FRAGMENTS OF THE DETERGENT OCTYL-TETRAOXYETHYLENE (C8E).
RfactorNum. reflection
Rwork0.167 -
obs0.167 16429
Displacement parametersBiso mean: 31.26 Å2
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2627 0 72 128 2827
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.687
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.01
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.212
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

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