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- PDB-1prn: REFINED STRUCTURE OF PORIN FROM RHODOPSEUDOMONAS BLASTICA AND COM... -

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Entry
Database: PDB / ID: 1prn
TitleREFINED STRUCTURE OF PORIN FROM RHODOPSEUDOMONAS BLASTICA AND COMPARISON WITH THE PORIN FROM RHODOBACTER CAPSULATUS
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 blasticus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.96 Å
AuthorsKreusch, A. / Schulz, G.E.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Refined structure of the porin from Rhodopseudomonas blastica. Comparison with the porin from Rhodobacter capsulatus.
Authors: Kreusch, A. / Schulz, G.E.
#1: Journal: Protein Sci. / Year: 1994
Title: The Structure of the Membrane Channel Porin from Rhodopseudomonas Blastica at 2.0 Angstroms Resolution
Authors: Kreusch, A. / Neubueser, A. / Schiltz, E. / Weckesser, J. / Schulz, G.E.
History
DepositionJul 13, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: 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_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_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 BY 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)31,5284
Polymers30,6091
Non-polymers9193
Water4,468248
1
A: PORIN
hetero molecules

A: PORIN
hetero molecules

A: PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,58512
Polymers91,8273
Non-polymers2,7589
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 area14530 Å2
ΔGint-68 kcal/mol
Surface area35440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.300, 104.300, 124.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Atom site foot note1: RESIDUES ILE 139 - SER 140 HAVE WEAK DENSITY.
2: THE STRUCTURE OF THE DETERGENT MOLECULES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY AND HAS THEREFORE BEEN PRELIMINARILY MODELED AS N-OCTYLTETRAOXYETHYLENE USED IN CRYSTALLIZATION.

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Components

#1: Protein PORIN /


Mass: 30608.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter blasticus (bacteria) / References: UniProt: P39767
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STRUCTURE OF THE DETERGENT MOLECULES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY AND HAS ...THE STRUCTURE OF THE DETERGENT MOLECULES COULD NOT BE IDENTIFIED FROM THE ELECTRON DENSITY AND HAS THEREFORE BEEN PRELIMINARILY MODELED AS N-OCTYLTETRAOXYETHYLENE USED IN CRYSTALLIZATION.
Sequence detailsTHE SEQUENCE IS DESCRIBED IN THE JRNL ARTICLE AND IN REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.26 Å3/Da / Density % sol: 71.13 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
220 mMTris-HCl1drop
3300 mM1dropLiCl
40.6 %(w/v)n-octyltetraoxyethylene1drop
53 mM1dropNaN3
610-18 %PEG6001drop
730-38 %(w/v)PEG6001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.96 Å / Lowest resolution: 100 Å / Num. obs: 35847 / % possible obs: 75 % / Observed criterion σ(I): 3 / Num. measured all: 291952 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 1.96 Å / Lowest resolution: 2 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.96→10 Å / σ(F): 0 / Details: RESIDUES ILE 139 - SER 140 HAVE WEAK DENSITY. /
RfactorNum. reflection
Rwork0.176 -
obs0.176 35620
Refinement stepCycle: LAST / Resolution: 1.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 63 248 2475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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
Num. reflection all: 35620 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 18 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_d2.91.8
X-RAY DIFFRACTIONx_dihedral_angle_d1.21.2
X-RAY DIFFRACTIONx_dihedral_angle_deg28.127.9

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