[English] 日本語
Yorodumi
- PDB-1lep: THREE-DIMENSIONAL STRUCTURE OF THE IMMUNODOMINANT HEAT-SHOCK PROT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lep
TitleTHREE-DIMENSIONAL STRUCTURE OF THE IMMUNODOMINANT HEAT-SHOCK PROTEIN CHAPERONIN-10 OF MYCOBACTERIUM LEPRAE
ComponentsCHAPERONIN-10
KeywordsCHAPERONE / ANTIGEN / HEAT SHOCK
Function / homology
Function and homology information


: / protein folding chaperone / unfolded protein binding / protein-folding chaperone binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Chaperonin GroES, conserved site / Chaperonins cpn10 signature. / Chaperonin 10 Kd subunit / GroES chaperonin family / GroES chaperonin superfamily / Chaperonin 10 Kd subunit / GroES-like superfamily
Similarity search - Domain/homology
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsMande, S.C. / Hol, W.G.J.
CitationJournal: Science / Year: 1996
Title: Structure of the heat shock protein chaperonin-10 of Mycobacterium leprae.
Authors: Mande, S.C. / Mehra, V. / Bloom, B.R. / Hol, W.G.
History
DepositionDec 13, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CHAPERONIN-10
B: CHAPERONIN-10
C: CHAPERONIN-10
D: CHAPERONIN-10
E: CHAPERONIN-10
F: CHAPERONIN-10
G: CHAPERONIN-10


Theoretical massNumber of molelcules
Total (without water)74,7757
Polymers74,7757
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.900, 129.000, 109.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99951, 0.027091, -0.01567), (-0.029152, 0.62379, -0.781048), (-0.011385, 0.781122, 0.624275)-1.1535, 34.1533, -15.7811
2given(0.996091, 0.071494, -0.051885), (-0.032423, -0.250465, -0.967583), (-0.082172, 0.965482, -0.247167)-1.2586, 67.7524, 2.7868
3given(0.994807, -0.01047, -0.101236), (0.034269, -0.902154, 0.43005), (-0.095833, -0.431286, -0.897111)2.1245, 52.7986, 66.8419
4given(0.991862, 0.027411, -0.124331), (-0.026686, -0.910098, -0.413534), (-0.124489, 0.413486, -0.90196)2.7442, 75.4921, 38.7526
5given(0.992447, -0.045716, -0.113837), (0.101872, -0.209857, 0.972411), (-0.068344, -0.976663, -0.203614)3.9951, 12.9744, 67.0067
6given(0.996987, -0.060926, -0.048002), (0.076101, 0.648739, 0.757197), (-0.014992, -0.758569, 0.651421)3.2498, -10.731, 35.7531

-
Components

#1: Protein
CHAPERONIN-10 / ML10 / Coordinate model: Cα atoms only


Mass: 10682.150 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Mycobacterium leprae (bacteria) / References: UniProt: P24301

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 55 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMMES1drop
21 mMEDTA1drop
31 mM1dropNaN3
4100 mMHEPES1reservoir
535 %(v/v)PEG4001reservoir
6150 mM1reservoirLiSO4

-
Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 3.5 Å / % possible obs: 98 %
Reflection shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.6 Å / % possible obs: 90 %

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 3.5→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.38 -
Rwork0.23 -
obs0.23 8733
Displacement parametersBiso mean: 40 Å2
Refinement stepCycle: LAST / Resolution: 3.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms567 0 0 0 567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

+
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