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- PDB-2prn: RHODOPSEUDOMONAS BLASTICA PORIN, TRIPLE MUTANT E1M, E99W, A116W -

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Basic information

Entry
Database: PDB / ID: 2prn
TitleRHODOPSEUDOMONAS BLASTICA PORIN, TRIPLE MUTANT E1M, E99W, A116W
ComponentsPORIN
KeywordsINTEGRAL MEMBRANE PROTEIN / PORIN / PORE EYELET MUTANT
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 / DIFFERENCE FOURIER / Resolution: 1.93 Å
AuthorsMaveyraud, L. / Schmid, B. / Schulz, G.E.
Citation
Journal: Protein Sci. / Year: 1998
Title: Porin mutants with new channel properties.
Authors: Schmid, B. / Maveyraud, L. / Kromer, M. / Schulz, G.E.
#1: Journal: FEBS Lett. / Year: 1996
Title: Expression of Porin from Rhodopseudomonas Blastica in Escherichia Coli Inclusion Bodies and Folding Into Exact Native Structure
Authors: Schmid, B. / Kroemer, M. / Schulz, G.E.
#2: 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.
History
DepositionJun 12, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
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)31,7275
Polymers30,7831
Non-polymers9444
Water1,928107
1
A: PORIN
hetero molecules

A: PORIN
hetero molecules

A: PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,18015
Polymers92,3493
Non-polymers2,83112
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 area14700 Å2
ΔGint-89 kcal/mol
Surface area35910 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.260, 104.260, 124.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein PORIN


Mass: 30783.162 Da / Num. of mol.: 1 / Mutation: E1M, E99W, A116W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter blasticus (bacteria) / Cell line: BL21 / Cellular location: OUTER MEMBRANE / Plasmid: PET-3B / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P39767
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.22 Å3/Da / Density % sol: 66 %
Crystal growpH: 7.8 / Details: pH 7.8
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

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→32.9 Å / Num. obs: 31332 / % possible obs: 81.5 % / Redundancy: 2.4 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 14.4
Reflection shellResolution: 1.93→2 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.189 / % possible all: 52
Reflection
*PLUS
Lowest resolution: 33 Å / % possible obs: 812 %
Reflection shell
*PLUS
% possible obs: 52 % / Num. unique obs: 1895

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1PRN

1prn


Resolution: 1.93→32.9 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflection
Rfree0.205 3135 10 %
Rwork0.184 --
obs-31264 81.5 %
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.93→32.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 64 107 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0290.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1470.3
X-RAY DIFFRACTIONp_mcbond_it0.8811.5
X-RAY DIFFRACTIONp_mcangle_it1.2041
X-RAY DIFFRACTIONp_scbond_it1.6341.5
X-RAY DIFFRACTIONp_scangle_it2.6913
X-RAY DIFFRACTIONp_plane_restr0.01630.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1470.3
X-RAY DIFFRACTIONp_planar_tor3.52
X-RAY DIFFRACTIONp_staggered_tor16.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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