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- PDB-3por: PORIN CONFORMATION IN THE ABSENCE OF CALCIUM; REFINED STRUCTURE A... -

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Basic information

Entry
Database: PDB / ID: 3por
TitlePORIN CONFORMATION IN THE ABSENCE OF CALCIUM; REFINED STRUCTURE AT 2.5 ANGSTROMS RESOLUTION
ComponentsPORIN
KeywordsINTEGRAL MEMBRANE PROTEIN PORIN
Function / homology
Function and homology information


porin activity / pore complex / monoatomic ion transport / cell outer membrane
Similarity search - Function
Gram-negative porin / Porin domain, Gram-negative type / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesRhodobacter capsulatus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWeiss, M.S. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Porin conformation in the absence of calcium. Refined structure at 2.5 A resolution.
Authors: Weiss, M.S. / Schulz, G.E.
#1: Journal: J.Mol.Biol. / Year: 1992
Title: Structure of Porin Refined at 1.8 Angstroms Resolution
Authors: Weiss, M.S. / Schulz, G.E.
#2: Journal: Science / Year: 1991
Title: Molecular Architecture and Electrostatic Properties of a Bacterial Porin
Authors: Weiss, M.S. / Abele, U. / Weckesser, J. / Welte, W. / Schiltz, E. / Schulz, G.E.
#3: Journal: Eur.J.Biochem. / Year: 1991
Title: Primary Structure of Porin from Rhodobacter Capsulatus
Authors: Schiltz, E. / Kreusch, A. / Nestel, U. / Schulz, G.E.
#4: Journal: FEBS Lett. / Year: 1991
Title: The Structure of Porin from Rhodobacter Capsulatus at 1.8 Angstroms Resolution
Authors: Weiss, M.S. / Kreusch, A. / Schiltz, E. / Nestel, U. / Welte, W. / Weckesser, J. / Schulz, G.E.
#5: Journal: J.Mol.Biol. / Year: 1991
Title: Crystals of an Integral Membrane Protein Diffracting to 1.8 Angstroms Resolution
Authors: Kreusch, A. / Weiss, M.S. / Welte, W. / Weckesser, J. / Schulz, G.E.
#6: Journal: FEBS Lett. / Year: 1990
Title: The Three-Dimensional Structure of Porin from Rhodobacter Capsulatus at 3 Angstroms Resolution
Authors: Weiss, M.S. / Wacker, T. / Weckesser, J. / Welte, W. / Schulz, G.E.
#7: Journal: FEBS Lett. / Year: 1989
Title: The Structure of Porin from Rhodobacter Capsulatus at 0.6 Nm Resolution
Authors: Weiss, M.S. / Wacker, T. / Nestel, U. / Woitzik, D. / Weckesser, J. / Kreutz, W. / Welte, W. / Schulz, G.E.
#8: Journal: FEBS Lett. / Year: 1989
Title: Crystallization and Preliminary X-Ray Analysis of Porin from Rhodobacter Capsulatus
Authors: Nestel, U. / Wacker, T. / Woitzik, D. / Weckesser, J. / Kreutz, W. / Welte, W.
History
DepositionNov 9, 1992Processing site: BNL
Revision 1.0Jul 15, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIXTEEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *S1* ON SHEET RECORDS BELOW IS ACTUALLY A SIXTEEN-STRANDED BETA-BARREL. THIS IS REPRESENTED AS A SEVENTEEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9843
Polymers31,5551
Non-polymers4292
Water1,38777
1
A: PORIN
hetero molecules

A: PORIN
hetero molecules

A: PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9529
Polymers94,6663
Non-polymers1,2866
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10700 Å2
ΔGint-53 kcal/mol
Surface area36200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)95.300, 95.300, 146.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Atom site foot note1: RESIDUE 117 IS A CIS PROLINE.
2: RESIDUE 545 HAS NOT BEEN UNAMBIGUOUSLY IDENTIFIED. IT HAS BEEN MODELED AS A DETERGENT N-OCTYLTETRAOXYETHYLENE.
3: FOURTEEN DETERGENT FRAGMENTS HAVE BEEN MODELED AS WATERS (SEE REMARK 5)
Components on special symmetry positions
IDModelComponents
11A-924-

HOH

21A-952-

HOH

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Components

#1: Protein PORIN


Mass: 31555.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / References: UniProt: P31243
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsFOURTEEN DETERGENT FRAGMENTS HAVE BEEN MODELED AS WATERS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1drop
220 mMTris-HCl1drop
3300 mM1dropLiCl
43 mM1dropNaN3
50.6 %(w/v)n-octyltetraoxyethylene1drop
67-10 %(w/v)PEG6001drop
723-30 %(w/v)PEG6001reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 9999 Å / Num. all: 69237 / Num. obs: 16568 / % possible obs: 95.1 % / Rmerge(I) obs: 0.052

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.5→10 Å / Rfactor Rwork: 0.188
Details: THE AUTHORS REFER TO THIS STRUCTURE AS CRYSTAL FORM-A'. RESIDUE 545 HAS NOT BEEN UNAMBIGUOUSLY IDENTIFIED. IT HAS BEEN MODELED AS A DETERGENT N-OCTYLTETRAOXYETHYLENE.
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 29 77 2325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
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_deg3.7
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 10 Å / Num. reflection obs: 16298 / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_dihedral_angle_deg1.5

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