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- PDB-1v9t: Structure of E. coli cyclophilin B K163T mutant bound to succinyl... -

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Basic information

Entry
Database: PDB / ID: 1v9t
TitleStructure of E. coli cyclophilin B K163T mutant bound to succinyl-ALA-PRO-ALA-P-nitroanilide
Components
  • (SIN)APA(NIT)
  • cyclophilin B
KeywordsISOMERASE/ISOMERASE INHIBITOR / BETA BARREL / ISOMERASE-ISOMERASE INHIBITOR complex
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
SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE / 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: 1.7 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
DepositionFeb 3, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Sep 5, 2012Group: Derived calculations
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cyclophilin B
B: cyclophilin B
C: (SIN)APA(NIT)


Theoretical massNumber of molelcules
Total (without water)36,6183
Polymers36,6183
Non-polymers00
Water3,261181
1
A: cyclophilin B


Theoretical massNumber of molelcules
Total (without water)18,0701
Polymers18,0701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cyclophilin B
C: (SIN)APA(NIT)


Theoretical massNumber of molelcules
Total (without water)18,5482
Polymers18,5482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.280, 79.280, 56.630
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein cyclophilin B


Mass: 18070.326 Da / Num. of mol.: 2 / 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: Protein/peptide (SIN)APA(NIT)


Type: Peptide-like / Class: Inhibitor / Mass: 477.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: SUCCINYL-ALA-PRO-ALA-P-NITROANILIDE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.71 Å3/Da / Density % sol: 54.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, methanol, sodium azide, Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jan 1, 1999
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→80 Å / Num. all: 40355 / Num. obs: 40355 / % possible obs: 92 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.238 / % possible all: 73.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1LOP

1lop


Resolution: 1.7→6 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.221 3972 RANDOM
Rwork0.184 --
all-39354 -
obs-39354 -
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 0 181 2712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_improper_angle_d1.23

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