[English] 日本語
Yorodumi
- PDB-1dkd: CRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dkd
TitleCRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PEPTIDE COMPLEX
Components
  • 12-MER PEPTIDE
  • GROEL
KeywordsCHAPERONE / MOLECULAR CHAPERON / HSP60 / PROTEIN FOLDING / PEPTIDE SELECTION / PHAGE DISPLAY / PEPTIDE BINDING GROOVE FORMED BY PAIRED HELICES SUBSTRATE PEPTIDE IN BETA-SHEET
Function / homology
Function and homology information


GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol
Similarity search - Function
GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family ...GroEL / GroEL / Chaperonin Cpn60, conserved site / Chaperonins cpn60 signature. / Chaperonin Cpn60/GroEL / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsChen, L. / Sigler, P.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity.
Authors: Chen, L. / Sigler, P.B.
History
DepositionDec 7, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GROEL
E: 12-MER PEPTIDE
B: GROEL
F: 12-MER PEPTIDE
C: GROEL
G: 12-MER PEPTIDE
D: GROEL
H: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)68,7608
Polymers68,7608
Non-polymers00
Water1,72996
1
A: GROEL
E: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-8 kcal/mol
Surface area7400 Å2
MethodPISA
2
B: GROEL
F: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area7450 Å2
MethodPISA
3
C: GROEL
G: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area940 Å2
ΔGint-7 kcal/mol
Surface area7590 Å2
MethodPISA
4
D: GROEL
H: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)17,1902
Polymers17,1902
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-7 kcal/mol
Surface area7630 Å2
MethodPISA
5
A: GROEL
E: 12-MER PEPTIDE
C: GROEL
G: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)34,3804
Polymers34,3804
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-27 kcal/mol
Surface area13550 Å2
MethodPISA
6
B: GROEL
F: 12-MER PEPTIDE

D: GROEL
H: 12-MER PEPTIDE


Theoretical massNumber of molelcules
Total (without water)34,3804
Polymers34,3804
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area3260 Å2
ΔGint-27 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.042, 134.668, 59.734
Angle α, β, γ (deg.)90.00, 94.38, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
GROEL / CHAPERONE HSP60


Mass: 15729.269 Da / Num. of mol.: 4 / Fragment: APICAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6F5
#2: Protein/peptide
12-MER PEPTIDE


Mass: 1460.676 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: the peptide was chemically synthesized and was SELECTED FROM PHAGE DISPLAY PEPTIDE LIBRARY.
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe peptide adopts a typical beta-turn; paired alpha helices H and I, and the groove between them ...The peptide adopts a typical beta-turn; paired alpha helices H and I, and the groove between them constitute the binding site.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4K, MgCl2, TrisCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-Cl1reservoir
2200 mM1reservoirMgCl2
330 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.923
DetectorType: BRANDEIS / Detector: CCD / Date: Sep 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.923 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 38529 / Num. obs: 35897 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2 % / Rmerge(I) obs: 0.303 / Num. unique all: 3394 / % possible all: 89.9
Reflection shell
*PLUS
% possible obs: 89.9 %

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementResolution: 2.1→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1783 -random
Rwork0.215 ---
all-38529 --
obs-35897 93.2 %-
Refinement stepCycle: LAST / Resolution: 2.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 0 96 4818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.32
X-RAY DIFFRACTIONc_bond_d0.007
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6

+
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