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- PDB-1opf: THE STRUCTURE OF OMPF PORIN IN A TETRAGONAL CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1opf
TitleTHE STRUCTURE OF OMPF PORIN IN A TETRAGONAL CRYSTAL FORM
ComponentsMATRIX PORIN OUTER MEMBRANE PROTEIN F
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / disordered domain specific binding / protein transport ...colicin transmembrane transporter activity / porin activity / pore complex / protein homotrimerization / monoatomic ion channel activity / monoatomic ion channel complex / cell outer membrane / lipopolysaccharide binding / 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. / Gram-negative porin / Porin domain, Gram-negative type / Porin, Gram-negative type / Porin / : / Porin domain superfamily / Porin ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Porin domain, Gram-negative type / 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: 3.2 Å
AuthorsCowan, S.W. / Schirmer, T. / Pauptit, R.A. / Jansonius, J.N.
Citation
#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.Struct.Biol. / Year: 1991
Title: A Common Channel-Forming Motif in Evolutionarily Distant Porins
Authors: Pauptit, R.A. / Schirmer, T. / Jansonius, J.N. / Rosenbusch, J.P. / Parker, M.W. / Tucker, A.D. / Tsernoglou, D. / Weiss, M.S. / Schulz, G.E.
#3: Journal: J.Cryst.Growth / Year: 1986
Title: The Growth and Characterization of Membrane Protein Crystals
Authors: Garavito, R.M. / Markovic-Housley, Z. / Jenkins, J.A.
#4: Journal: J.Mol.Biol. / Year: 1983
Title: X-Ray Diffraction Analysis of Matrix Porin, an Integral Membrane Protein from Escherichia Coli Outer Membranes
Authors: Garavito, R.M. / Jenkins, J. / Jansonius, J.N. / Karlsson, R. / Rosenbusch, J.P.
#5: Journal: J.Cell Biol. / Year: 1980
Title: Three-Dimensional Crystals of an Integral Membrane Protein: An Initial X-Ray Analysis
Authors: Garavito, R.M. / Rosenbusch, J.P.
History
DepositionNov 21, 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: Version format compliance
Revision 1.3Feb 22, 2012Group: Database references
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MATRIX PORIN OUTER MEMBRANE PROTEIN F
B: MATRIX PORIN OUTER MEMBRANE PROTEIN F
C: MATRIX PORIN OUTER MEMBRANE PROTEIN F
D: MATRIX PORIN OUTER MEMBRANE PROTEIN F
E: MATRIX PORIN OUTER MEMBRANE PROTEIN F
F: MATRIX PORIN OUTER MEMBRANE PROTEIN F


Theoretical massNumber of molelcules
Total (without water)222,6866
Polymers222,6866
Non-polymers00
Water00
1
A: MATRIX PORIN OUTER MEMBRANE PROTEIN F
B: MATRIX PORIN OUTER MEMBRANE PROTEIN F
C: MATRIX PORIN OUTER MEMBRANE PROTEIN F


Theoretical massNumber of molelcules
Total (without water)111,3433
Polymers111,3433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-50 kcal/mol
Surface area40150 Å2
MethodPISA
2
D: MATRIX PORIN OUTER MEMBRANE PROTEIN F
E: MATRIX PORIN OUTER MEMBRANE PROTEIN F
F: MATRIX PORIN OUTER MEMBRANE PROTEIN F


Theoretical massNumber of molelcules
Total (without water)111,3433
Polymers111,3433
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8610 Å2
ΔGint-55 kcal/mol
Surface area40170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.900, 154.900, 172.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1187, 0.98614, -0.11593), (-0.01757, 0.11466, 0.99325), (0.99277, 0.11994, 0.00371)86.74791, 1.46502, -77.10458
2given(-0.11837, -0.01763, 0.99281), (0.98615, 0.11492, 0.11961), (-0.1162, 0.99322, 0.00379)86.83439, -76.4758, 8.91059
3given(-0.97362, -0.22814, -0.0029), (-0.22814, 0.97363, 2.0E-5), (0.00282, 0.00068, -1)152.8905, 17.64569, -0.29894
4given(0.11662, -0.98667, -0.11347), (0.00996, -0.11308, 0.99354), (-0.99313, -0.11699, -0.00336)68.31725, -0.72167, 77.05116
5given(-0.10915, -0.01198, -0.99395), (0.98717, 0.11591, -0.1098), (0.11653, -0.99319, -0.00083)85.74075, -76.62802, -9.01502
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO TRIMERS. THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE OTHER FIVE MONOMERS IN THE ASYMMETRIC UNIT WHEN APPLIED TO THE COORDINATES IN THIS ENTRY.

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Components

#1: Protein
MATRIX PORIN OUTER MEMBRANE PROTEIN F


Mass: 37114.250 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02931

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.64 Å3/Da / Density % sol: 73.48 %
Crystal grow
*PLUS
Temperature: 21-23 ℃ / Method: vapor diffusion
Details: Garavito, R.M., (1986) Methods Enzymol., 125, 309.
PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16-9 mg/mlprotein1drop
27.5 %(w/v)PEG20001drop
320-50 mMsodium phosphate1drop
40.8 %(w/v)octylglucoside1drop
50.08 %(w/v)detergent1drop
60.01 %(w/v)1dropNaN3
715 %PEG20001reservoir
840-500 mM1reservoirNaCl
940-100 mMsodium phosphate1reservoir
100.01 %1reservoirNaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 56516 / % possible obs: 87 %
Reflection
*PLUS
Highest resolution: 3.2 Å / Redundancy: 2.4 % / Num. measured all: 133465 / Rmerge(I) obs: 0.125

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.2→10 Å /
RfactorNum. reflection
Rwork0.241 -
obs0.241 55523
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15762 0 0 0 15762
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_deg1.581
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

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