[English] 日本語
Yorodumi
- PDB-5yb9: Crystal structure of a dimeric cyclophilin A from T.vaginalis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yb9
TitleCrystal structure of a dimeric cyclophilin A from T.vaginalis
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Cyclophilin A / Divergent loop cyclophilin / Dimeric cyclophilin
Function / homology
Function and homology information


cyclosporin A binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / cytoplasm
Similarity search - Function
Cyclophilin-like / Cyclophilin / Cyclophilin-type peptidyl-prolyl cis-trans isomerase / 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
Similarity search - Component
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.276 Å
AuthorsCho, C.C. / Lin, M.H. / Chou, C.C. / Martin, T. / Chen, C. / Hsu, C.H.
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis
Authors: Martin, T. / Lou, Y.C. / Chou, C.C. / Wei, S.Y. / Sadotra, S. / Cho, C.C. / Lin, M.H. / Tai, J.H. / Hsu, C.H. / Chen, C.
History
DepositionSep 4, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Derived calculations
Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.identifier_ORCID / _pdbx_struct_oper_list.matrix[1][1] ..._citation_author.identifier_ORCID / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[3]
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase


Theoretical massNumber of molelcules
Total (without water)19,3581
Polymers19,3581
Non-polymers00
Water84747
1
A: Peptidyl-prolyl cis-trans isomerase

A: Peptidyl-prolyl cis-trans isomerase


  • defined by author
  • Evidence: light scattering, Size-exclusion chromatography with multi-angle light scattering, equilibrium centrifugation, Analytical ultra centrifugation- sedimentation velocity experiments also ...Evidence: light scattering, Size-exclusion chromatography with multi-angle light scattering, equilibrium centrifugation, Analytical ultra centrifugation- sedimentation velocity experiments also confirm dimeric nature of TvCyP1
  • 38.7 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)38,7172
Polymers38,7172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Unit cell
Length a, b, c (Å)38.505, 38.505, 365.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase / PPIase


Mass: 19358.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cyclophilin A / Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_004440 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A2DT06, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.15 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100 mM HEPES pH 7.0, 30% (v/v) Jeffamine M-600

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9998 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 2.27→29.254 Å / Num. obs: 8106 / % possible obs: 90 % / Redundancy: 3.7 % / Net I/σ(I): 6.18
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 2.107 / Rsym value: 0.415 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DYW

1dyw


Resolution: 2.276→29.254 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.05
RfactorNum. reflection% reflection
Rfree0.2864 752 10.01 %
Rwork0.212 --
obs0.2189 7511 89.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.276→29.254 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 0 47 1378
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081360
X-RAY DIFFRACTIONf_angle_d0.9081823
X-RAY DIFFRACTIONf_dihedral_angle_d9.519809
X-RAY DIFFRACTIONf_chiral_restr0.057191
X-RAY DIFFRACTIONf_plane_restr0.007239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2765-2.45220.33581050.2107949X-RAY DIFFRACTION67
2.4522-2.69880.29431430.22881281X-RAY DIFFRACTION89
2.6988-3.08890.2881590.21341435X-RAY DIFFRACTION97
3.0889-3.89030.26791660.19461495X-RAY DIFFRACTION98
3.8903-29.25650.2881790.21871599X-RAY DIFFRACTION96

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more