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- PDB-1pho: CRYSTAL STRUCTURES EXPLAIN FUNCTIONAL PROPERTIES OF TWO E. COLI PORINS -

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Entry
Database: PDB / ID: 1pho
TitleCRYSTAL STRUCTURES EXPLAIN FUNCTIONAL PROPERTIES OF TWO E. COLI PORINS
ComponentsPHOSPHOPORIN
KeywordsOUTER MEMBRANE PROTEIN
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 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 PhoE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsSchirmer, T. / Cowan, S.W. / Jansonius, J.N.
Citation
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.
#1: 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.
#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.
History
DepositionJan 15, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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 / 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: PHOSPHOPORIN


Theoretical massNumber of molelcules
Total (without water)36,8711
Polymers36,8711
Non-polymers00
Water00
1
A: PHOSPHOPORIN

A: PHOSPHOPORIN

A: PHOSPHOPORIN


Theoretical massNumber of molelcules
Total (without water)110,6143
Polymers110,6143
Non-polymers00
Water0
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 area8560 Å2
ΔGint-60 kcal/mol
Surface area40730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)119.900, 119.900, 51.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Atom site foot note1: THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE: ASP 25, ASN 26, ALA 32, ...1: THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE: ASP 25, ASN 26, ALA 32, SER 33, ASP 181, PHE 182, GLY 183, ASP 184, ASN 198, GLU 199, SER 204, GLY 249, ASP 319, SER 320, AND ASP 321.

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Components

#1: Protein PHOSPHOPORIN


Mass: 36871.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / References: UniProt: P02932
Sequence detailsTHESE COORDINATES ARE IN AN INTERMEDIATE STAGE OF REFINEMENT AND WILL BE UPDATED SOON. THE RESIDUE ...THESE COORDINATES ARE IN AN INTERMEDIATE STAGE OF REFINEMENT AND WILL BE UPDATED SOON. THE RESIDUE NUMBERING IS BASED ON THE HOMOLOGOUS MATRIX PORIN (OMPF). CONSEQUENTLY, THERE ARE GAPS IN THE NUMBERING (27-31,75-76,242-247) AND INSERTIONS (121A,183A AND 183B).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal grow
*PLUS
pH: 9.8 / Method: microdialysis
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
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 8685 / % possible obs: 95 % / Rmerge(I) obs: 0.09

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→8 Å / Rfactor Rwork: 0.222 / Rfactor obs: 0.222
Details: ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY HAVE A WEIGHT OF ZERO. THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED ...Details: ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY HAVE A WEIGHT OF ZERO. THE FOLLOWING RESIDUES COULD NOT BE MODELLED DUE TO WEAK OR NONEXISTENT ELECTRON DENSITY AND ARE INCLUDED IN THE MODEL IN AN ARBITRARY CONFORMATION ONLY FOR CONVENIENCE: 25-33 181-184 198-199 204 249 319-321
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 0 0 2602
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
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_deg3.9
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
Highest resolution: 3 Å / Lowest resolution: 8 Å / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.9

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