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- PDB-8prn: E1M, K50A, R52A, D97A, E99A MUTANT OF RH. BLASTICA PORIN -

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Basic information

Entry
Database: PDB / ID: 8prn
TitleE1M, K50A, R52A, D97A, E99A MUTANT OF RH. BLASTICA PORIN
ComponentsPORIN
KeywordsMEMBRANE PROTEIN / INTEGRAL 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: 2.3 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. / Kromer, 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 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2844
Polymers30,3651
Non-polymers9193
Water1,76598
1
A: PORIN
hetero molecules

A: PORIN
hetero molecules

A: PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,85212
Polymers91,0943
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-71 kcal/mol
Surface area35540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.750, 103.750, 124.950
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: 30364.674 Da / Num. of mol.: 1 / Mutation: E1M, K50A, R52A, D97A, E99A
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-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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 4.26 Å3/Da / Density % sol: 66 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Kreusch, A., (1994) J.Mol.Biol., 243, 891.
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: Dec 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→12.8 Å / Num. obs: 34853 / % possible obs: 85.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 15.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.19 / % possible all: 51
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 26 Å / Num. obs: 20686 / % possible obs: 93 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.38 Å / % possible obs: 72 % / Redundancy: 1.4 % / Num. unique obs: 1565 / Rmerge(I) obs: 0.185

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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: 2.3→25.9 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2095 10 %SAME AS WILD-TYPE
Rwork0.177 ---
obs-20686 92.9 %-
Displacement parametersBiso mean: 32.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2146 0 63 98 2307
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0360.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord0.1740.3
X-RAY DIFFRACTIONp_mcbond_it1.351.5
X-RAY DIFFRACTIONp_mcangle_it1.7391
X-RAY DIFFRACTIONp_scbond_it2.6741.5
X-RAY DIFFRACTIONp_scangle_it3.9673
X-RAY DIFFRACTIONp_plane_restr0.01970.02
X-RAY DIFFRACTIONp_chiral_restr0.1590.15
X-RAY DIFFRACTIONp_singtor_nbd0.1860.3
X-RAY DIFFRACTIONp_multtor_nbd0.2490.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1740.3
X-RAY DIFFRACTIONp_planar_tor4.12
X-RAY DIFFRACTIONp_staggered_tor19.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.620
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.177
Solvent computation
*PLUS
Displacement parameters
*PLUS

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