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- PDB-1gfn: OMPF PORIN DELETION (MUTANT DELTA 109-114) -

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Basic information

Entry
Database: PDB / ID: 1gfn
TitleOMPF PORIN DELETION (MUTANT DELTA 109-114)
ComponentsMATRIX PORIN OUTER MEMBRANE PROTEIN F
KeywordsTRANSMEMBRANE PROTEIN / OUTER MEMBRANE / 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 channel activity / 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 channel activity / lipopolysaccharide binding / cell outer membrane / disordered domain specific binding / protein transport / monoatomic ion transmembrane transport / 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 ...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: 3.1 Å
AuthorsLou, K.-L. / Schirmer, T.
Citation
Journal: J.Biol.Chem. / Year: 1996
Title: Structural and functional characterization of OmpF porin mutants selected for larger pore size. I. Crystallographic analysis.
Authors: Lou, K.L. / Saint, N. / Prilipov, A. / Rummel, G. / Benson, S.A. / Rosenbusch, J.P. / Schirmer, T.
#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: 1988
Title: Mutations that Alter the Pore Function of the Ompf Porin of Escherichia Coli K12
Authors: Benson, S.A. / Occi, J.L. / Sampson, B.A.
History
DepositionMay 8, 1996Processing site: BNL
Revision 1.0Dec 7, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 18, 2018Group: Advisory / Data collection / Other
Category: diffrn_detector / pdbx_database_status ...diffrn_detector / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _struct_ref_seq_dif.details / _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)40,11113
Polymers36,4331
Non-polymers3,67712
Water2,324129
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)120,33239
Polymers109,3003
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 area15410 Å2
ΔGint45 kcal/mol
Surface area45030 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)117.700, 117.700, 52.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

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Components

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


Mass: 36433.488 Da / Num. of mol.: 1 / Mutation: DEL(109-114)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: OC 1509 / Production host: 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.: 129 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE HET RESIDUES 341 - 354 HAVE NOT BEEN IDENTIFIED UNAMBIGUOUSLY AND HAVE BEEN MODELED AS ...THE HET RESIDUES 341 - 354 HAVE NOT BEEN IDENTIFIED UNAMBIGUOUSLY AND HAVE BEEN MODELED AS FRAGMENTS OF THE DETERGENT OCTYL-TETRAOXYETHYLENE (C8E).
Sequence detailsRESIDUES LEU 109 TO MET 114 ARE ABSENT IN THIS COORDINATE SET DUE TO THE DELETION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.47 %
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
210.5 %PEG200012

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Data collection

DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Dec 9, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 7211 / % possible obs: 97.8 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.09
Reflection
*PLUS
Highest resolution: 3.1 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction
X-PLORphasing
RefinementResolution: 3.1→8 Å
Details: THE MUTANT MODEL IS BASED ON THE WILD-TYPE MODEL, PDB ENTRY 2OMF. IN PARTICULAR, ALL WATER MOLECULES (EXCEPT IN THE VICINITY OF THE SITE OF MUTATION) AND THE DETERGENT FRAGMENTS HAVE BEEN ...Details: THE MUTANT MODEL IS BASED ON THE WILD-TYPE MODEL, PDB ENTRY 2OMF. IN PARTICULAR, ALL WATER MOLECULES (EXCEPT IN THE VICINITY OF THE SITE OF MUTATION) AND THE DETERGENT FRAGMENTS HAVE BEEN TAKEN FROM THE WILD-TYPE MODEL 2OMF. 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).
RfactorNum. reflection
Rwork0.19 -
obs0.19 7211
Displacement parametersBiso mean: 27.11 Å2
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2532 0 72 129 2733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.705
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: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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