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- PDB-1j2a: Structure of E. coli cyclophilin B K163T mutant -

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Basic information

Entry
Database: PDB / ID: 1j2a
TitleStructure of E. coli cyclophilin B K163T mutant
Componentscyclophilin B
KeywordsISOMERASE / BETA BARREL
Function / homology
Function and homology information


protein peptidyl-prolyl isomerization / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase, E. coli cyclophilin A-like / Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase A / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsKonno, M. / Sano, Y. / Okudaira, K. / Kawaguchi, Y. / Yamagishi-Ohmori, Y. / Fushinobu, S. / Matsuzawa, H.
CitationJournal: Eur.J.Biochem. / Year: 2004
Title: Escherichia coli cyclophilin B binds a highly distorted form of trans-prolyl peptide isomer
Authors: Konno, M. / Sano, Y. / Okudaira, K. / Kawaguchi, Y. / Yamagishi-Ohmori, Y. / Fushinobu, S. / Matsuzawa, H.
History
DepositionDec 26, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cyclophilin B


Theoretical massNumber of molelcules
Total (without water)18,0701
Polymers18,0701
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.55, 82.55, 52.35
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein cyclophilin B


Mass: 18070.326 Da / Num. of mol.: 1 / Mutation: K163T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pATrp EPPIa / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: P20752, UniProt: P0AFL3*PLUS, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19.5 mg/mlprotein1drop
238 %(w/v)satammonium sulfate1drop
30.04 %(w/v)1dropNaN3
480 mMTris-HCl1droppH8.0
546 %(w/v)satammonium sulfate1reservoir
60.04 %(w/v)1reservoirNaN3
7100 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 6, 2000
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 19219 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.8
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.402 / % possible all: 96.5
Reflection
*PLUS
Num. measured all: 133992
Reflection shell
*PLUS
% possible obs: 96.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1J28

1j28
PDB Unreleased entry


Resolution: 1.8→8 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.225 1868 RANDOM
Rwork0.201 --
obs-18959 -
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 0 81 1354
Refinement
*PLUS
Lowest resolution: 8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.006
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg0.842
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.82 Å / Rfactor Rfree: 0.311 / Rfactor Rwork: 0.287

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