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- PDB-1vai: Structure of e. coli cyclophilin B K163T mutant bound to n-acetyl... -

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Basic information

Entry
Database: PDB / ID: 1vai
TitleStructure of e. coli cyclophilin B K163T mutant bound to n-acetyl-ala-ala-pro-ala-7-amino-4-methylcoumarin
Components
  • (ACE)AAPA(MCM)
  • cyclophilin 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
ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARINN / 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
DepositionFeb 17, 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: Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 23, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cyclophilin B
B: cyclophilin B
C: (ACE)AAPA(MCM)


Theoretical massNumber of molelcules
Total (without water)36,6523
Polymers36,6523
Non-polymers00
Water3,549197
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
MethodPISA
2
B: cyclophilin B
C: (ACE)AAPA(MCM)


Theoretical massNumber of molelcules
Total (without water)18,5822
Polymers18,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.730, 78.730, 56.160
Angle α, β, γ (deg.)90.00, 90.00, 120.0
Int Tables number145
Space group name H-MP32

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Components

#1: Protein cyclophilin B / PPIase A / Rotamase A / Cyclophilin A


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 (ACE)AAPA(MCM)


Type: Peptide-like / Class: Inhibitor / Mass: 511.570 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED / References: ACE-ALA-ALA-PRO-ALA-7-AMINO-4-METHYLCOUMARINN
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: AMMONIUM SULPHATE, 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: Dec 20, 1998
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: 35961 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.88 Å / Rmerge(I) obs: 0.371 / % possible all: 97.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 1V9T

1v9t


Resolution: 1.8→6 Å / σ(F): 2
RfactorNum. reflectionSelection details
Rfree0.229 3469 RANDOM
Rwork0.188 --
obs-34891 -
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2518 0 0 197 2715
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.38
X-RAY DIFFRACTIONx_improper_angle_d0.75

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