[English] 日本語
Yorodumi
- PDB-6l2b: Crystal structure of cyclophilin mutant I164M from Leishmania don... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l2b
TitleCrystal structure of cyclophilin mutant I164M from Leishmania donovani at 2.65 angstrom resolution
ComponentsPeptidyl-prolyl cis-trans isomerase
KeywordsISOMERASE / Peptidyl prolyl isomerase / Cyclophilin
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding
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 speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGhosh, S. / Biswas, G. / Datta, A.K. / Banerjee, R.
Citation
Journal: To Be Published
Title: Crystal structure of cyclophilin mutant I164M from Leishmania donovani at 2.65 angstrom resolution.
Authors: Ghosh, S. / Biswas, G. / Datta, A.K. / Banerjee, R.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2007
Title: Structure of cyclophilin from Leishmania donovani at 1.97 A resolution.
Authors: Venugopal, V. / Sen, B. / Datta, A.K. / Banerjee, R.
History
DepositionOct 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 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)19,1091
Polymers19,1091
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7630 Å2
Unit cell
Length a, b, c (Å)48.618, 48.618, 141.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

-
Components

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


Mass: 19108.578 Da / Num. of mol.: 1 / Mutation: I164M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: CYP / Plasmid: pQE32 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: Q9U9R3, peptidylprolyl isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.15 Å3/Da / Density % sol: 42.9 % / Description: Tetragonal bipyramid
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20mM Tris HCl, 100mM NaCl, 0.02% sodium azide, PEG 3350 (Reservoir 30% and precipitant 3% in the final drop), protein at concentration 5 mg/ml.

-
Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5406 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2019
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.65→45.97 Å / Num. obs: 5381 / % possible obs: 99.83 % / Redundancy: 5.58 % / Biso Wilson estimate: 44.16 Å2 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.112 / Χ2: 1.15 / Net I/σ(I): 10.3
Reflection shellResolution: 2.651→2.746 Å / Redundancy: 5.58 % / Rmerge(I) obs: 0.102 / Num. unique obs: 5384 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
CrystalClear2data reduction
CrystalClear2data scaling
CrystalClear2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAQ

2haq


Resolution: 2.65→45.97 Å / SU ML: 0.3601 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 15.4865
RfactorNum. reflection% reflectionSelection details
Rfree0.223 269 5 %Random selection
Rwork0.1775 ---
obs-5381 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.65 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 0 41 1315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00231304
X-RAY DIFFRACTIONf_angle_d0.51031763
X-RAY DIFFRACTIONf_chiral_restr0.0472192
X-RAY DIFFRACTIONf_plane_restr0.0033232
X-RAY DIFFRACTIONf_dihedral_angle_d2.6326761
LS refinement shellResolution: 2.651→2.7457 Å
RfactorNum. reflection% reflection
Rfree0.3029 129 -
Rwork0.2124 2467 -
obs--99.92 %

+
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