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- PDB-1k6k: Crystal Structure of ClpA, an AAA+ Chaperone-like Regulator of Cl... -

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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 / ATP binding / cytosol / cytoplasm
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / 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 amino terminal domain, pathogenicity island component ...Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / 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 amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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