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- PDB-1h6s: Asymmetric conductivity of engineered proteins -

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Basic information

Entry
Database: PDB / ID: 1h6s
TitleAsymmetric conductivity of engineered proteins
ComponentsPORIN
KeywordsMEMBRANE PROTEIN / INTEGRAL 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 speciesRHODOPSEUDOMONAS BLASTICA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBannwarth, M. / Schulz, G.E.
CitationJournal: Protein Eng. / Year: 2002
Title: Asymmetric Conductivity of Engineered Porins
Authors: Bannwarth, M. / Schulz, G.E.
History
DepositionJun 22, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "1A" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "1A" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-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
1: PORIN


Theoretical massNumber of molelcules
Total (without water)32,2231
Polymers32,2231
Non-polymers00
Water00
1
1: PORIN

1: PORIN

1: PORIN


Theoretical massNumber of molelcules
Total (without water)96,6683
Polymers96,6683
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
MethodPQS
Unit cell
Length a, b, c (Å)104.200, 104.200, 124.900
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: 32222.725 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: INSERT SEQUENCE, GGGGPKLAKMEKARGGGG / Source: (gene. exp.) RHODOPSEUDOMONAS BLASTICA (bacteria)
Description: RECOMBINANT ESCHERICHIA COLI. SYNTHETIC DNA INSERTION
Plasmid: PET-3B-INS41L / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39767
Compound detailsCHAIN 1 AN 18 AMINO ACID INSERTION BETWEEN ASN 203 AND ASP 203 CHAIN 1 ENGINEERED MUTAION E1M: ...CHAIN 1 AN 18 AMINO ACID INSERTION BETWEEN ASN 203 AND ASP 203 CHAIN 1 ENGINEERED MUTAION E1M: EXPRESSION SYSTEM

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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: 4.05 Å3/Da / Density % sol: 69.63 %
Crystal growpH: 4.8
Details: 50 MM NAOAC PH 4.75, 100 MM (NH4)2SO4, 5.5 % PEG4000
Crystal grow
*PLUS
pH: 4.75 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mM1droppH4.75NaOAc
2100 mMammonium sulfate1drop
35.5 %PEG40001drop
45 mMoctyltetraoxyethylene1drop
512.5 mMdecanoyl sucrose1drop
65 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: IMAGE PLATE / Date: Oct 14, 2000
RadiationMonochromator: NI-FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→36 Å / Num. obs: 10136 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 6.6 % / Biso Wilson estimate: 37.904 Å2 / Net I/σ(I): 19.1
Reflection shellResolution: 3→3.03 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 5.1 / % possible all: 99
Reflection
*PLUS
% possible obs: 99 % / Num. measured all: 66659 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.15 Å / Num. unique obs: 1498 / Num. measured obs: 9696 / Rmerge(I) obs: 0.184

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PRN

1prn


Resolution: 3→36 Å / Data cutoff high absF: 10000 / Cross valid method: RMSD / σ(F): 3
Details: INSERT REGION IS DISORDERED ONLY MISSING BOND IN COMPARISON TO WT IS SEEN.
RfactorNum. reflection% reflection
Rfree0.21 538 5.3 %
Rwork0.197 --
obs0.197 66659 99 %
Displacement parametersBiso mean: 22.268 Å2
Refine analyzeLuzzati coordinate error obs: 0.2882 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.2253 Å
Refinement stepCycle: LAST / Resolution: 3→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2164 0 0 0 2164
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006533
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.28038
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.47026
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.5945
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.297 60 5.3 %
Rwork0.234 957 -
obs--99 %
Refinement
*PLUS
Rfactor Rfree: 0.297 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.47026
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.5945

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