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- PDB-1mpf: STRUCTURAL AND FUNCTIONAL ALTERATIONS OF A COLICIN RESISTANT MUTA... -

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Basic information

Entry
Database: PDB / ID: 1mpf
TitleSTRUCTURAL AND FUNCTIONAL ALTERATIONS OF A COLICIN RESISTANT MUTANT OF OMPF-PORIN FROM ESCHERICHIA COLI
ComponentsMATRIX PORIN OUTER MEMBRANE PROTEIN F
KeywordsMEMBRANE 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 / protein transport ...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 / protein transport / monoatomic ion channel activity / lipid binding / identical protein binding / membrane
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 (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsSchirmer, T.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Structural and functional alterations of a colicin-resistant mutant of OmpF porin from Escherichia coli.
Authors: Jeanteur, D. / Schirmer, T. / Fourel, D. / Simonet, V. / Rummel, G. / Widmer, C. / Rosenbusch, J.P. / Pattus, F. / Pages, J.M.
#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.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Feb 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 14, 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 / pdbx_database_status / struct_ref_seq_dif / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS *A1* AND *A2* ARE DEFINED. STRANDS 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 AND 15 ARE IDENTICAL.

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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)40,85013
Polymers37,1721
Non-polymers3,67712
Water2,342130
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)122,54939
Polymers111,5173
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 area15450 Å2
ΔGint41 kcal/mol
Surface area43550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.900, 117.900, 52.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Atom site foot note1: RESIDUE 27 COULD NOT BE MODELED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND IS INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE.
2: HET RESIDUES 341 - 354 HAVE NOT BEEN IDENTIFIED UNAMBIGOUSLY AND HAVE BEEN MODELED AS FRAGMENTS OF THE DETERGENT OCTYL-TETRAOXYETHYLENE (ABBREVIATED C8E).

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Components

#1: Protein MATRIX PORIN OUTER MEMBRANE PROTEIN F


Mass: 37172.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.83 %
Crystal grow
*PLUS
pH: 9.8 / Method: microdialysis / Details: Pauptit, R. A., (1991) J. Mol. Biol., 218, 505.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
20.05 MTris-HCl1reservoir
30.6 %(w/w)n-octyl-2-hydroxyethylsulfoxide1reservoir
40.1 %octylPOE1reservoir
50.7 M1reservoirMgCl2
66 %(w/w)PEG20001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7337 / % possible obs: 84.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→8 Å
Details: NO INDIVIDUAL B-FACTOR REFINEMENT; B-FACTORS OF THE MUTATED RESIDUE ASP 119 WERE MANUALLY SET TO 45 A**2 ACCORDING TO DIFFERENCE-FOURIER DENSITY. ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ...Details: NO INDIVIDUAL B-FACTOR REFINEMENT; B-FACTORS OF THE MUTATED RESIDUE ASP 119 WERE MANUALLY SET TO 45 A**2 ACCORDING TO DIFFERENCE-FOURIER DENSITY. ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY HAVE AN OCCUPANCY OF ZERO. RESIDUE 27 COULD NOT BE MODELED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND IS INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE. HET RESIDUES 341 - 354 HAVE NOT BEEN IDENTIFIED UNAMBIGOUSLY AND HAVE BEEN MODELED AS FRAGMENTS OF THE DETERGENT OCTYL- TETRAOXYETHYLENE (ABBREVIATED C8E).
RfactorNum. reflection
Rwork0.166 -
obs0.166 6915
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 72 130 2833
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_deg1.8
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_d
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.8

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