[English] 日本語
Yorodumi
- PDB-1k6k: Crystal Structure of ClpA, an AAA+ Chaperone-like Regulator of Cl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1k6k
TitleCrystal Structure of ClpA, an AAA+ Chaperone-like Regulator of ClpAP protease implication to the functional difference of two ATPase domains
ComponentsATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA
KeywordsHYDROLASE / ClpA / chaperone / ATPase / adaptor binding / N-domain
Function / homology
Function and homology information


endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / cellular response to heat / response to oxidative stress / ATP hydrolysis activity / proteolysis / ATP binding / cytosol / cytoplasm
Similarity search - Function
ATP-dependent Clp protease ATP-binding subunit ClpA / Double Clp-N motif / Clp, N-terminal domain / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain ...ATP-dependent Clp protease ATP-binding subunit ClpA / Double Clp-N motif / Clp, N-terminal domain / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGuo, F. / Maurizi, M.R. / Esser, L. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of ClpA, an HSP100 chaperone and regulator of ClpAP protease
Authors: Guo, F. / Maurizi, M.R. / Esser, L. / Xia, D.
History
DepositionOct 16, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA


Theoretical massNumber of molelcules
Total (without water)16,2001
Polymers16,2001
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.021, 51.965, 65.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

-
Components

#1: Protein ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA / ATP-binding component of serine protease / endopeptidase Clp ATP-binding chain A


Mass: 16200.268 Da / Num. of mol.: 1 / Fragment: N-terminal, residues 1-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 1.88 Å3/Da / Density % sol: 34.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: VAPOR DIFFUSION, HANGING DROP, pH 7.0 at 294K
Crystal grow
*PLUS
Temperature: 21.5-22.5 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
160 %ammonium sulfate1drop
220 mMHEPES1droppH7.5
30.1 MPIPES1reservoirpH7.0
435 %PEG80001reservoir
50.32 Msodium citrate1reservoir

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineTypeID
SYNCHROTRONNSLS X9B1
SYNCHROTRONAPS APS 2
SYNCHROTRONAPS 5ID-B3
Detector
TypeIDDetector
ADSC QUANTUM 41CCD
MARRESEARCH2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→14 Å / Num. obs: 7959 / % possible obs: 67.4 % / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 14 Å / Num. obs: 7990 / % possible obs: 67.2 % / Rmerge(I) obs: 0.028
Reflection shell
*PLUS
% possible obs: 21.1 % / Rmerge(I) obs: 0.199

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ClpA N-domain

Resolution: 1.8→14 Å / Cross valid method: THROUGHOUT /
RfactorSelection details
Rfree0.2626 random
Rwork0.2136 -
Refinement stepCycle: LAST / Resolution: 1.8→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1124 0 0 69 1193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004875
X-RAY DIFFRACTIONx_angle_deg1.00808
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.263 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.01
LS refinement shell
*PLUS
Rfactor Rfree: 0.336 / Rfactor Rwork: 0.283

+
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