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- PDB-1mbv: CRYSTAL STRUCTURE ANALYSIS OF ClpSN HETERODIMER TETRAGONAL FORM -

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Basic information

Entry
Database: PDB / ID: 1mbv
TitleCRYSTAL STRUCTURE ANALYSIS OF ClpSN HETERODIMER TETRAGONAL FORM
Components
  • ATP-Dependent clp Protease ATP-Binding Subunit clp A
  • Protein yljA
KeywordsPROTEIN BINDING / Adaptors / Hsp100/Clp chaperone / AAA+ family ATP-dependent protease
Function / homology
Function and homology information


endopeptidase Clp complex / molecular function inhibitor activity / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / protein-folding chaperone binding / cellular response to heat / response to heat / response to oxidative stress ...endopeptidase Clp complex / molecular function inhibitor activity / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / protein unfolding / protein catabolic process / protein-folding chaperone binding / cellular response to heat / response to heat / response to oxidative stress / ATP hydrolysis activity / proteolysis / ATP binding / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA / ATP-dependent Clp protease adaptor protein ClpS / Double Clp-N motif / Clp, N-terminal domain / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / ClpA/B, conserved site 2 / Chaperonins clpA/B signature 2. ...Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA / ATP-dependent Clp protease adaptor protein ClpS / Double Clp-N motif / Clp, N-terminal domain / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / 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 / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease adapter protein ClpS / ATP-dependent Clp protease ATP-binding subunit ClpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsGuo, F. / Esser, L. / Singh, S.K. / Maurizi, M.R. / Xia, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of the Heterodimeric Complex of the Adaptor, ClpS, with the N-domain of AAA+ Chaperone ClpA
Authors: Guo, F. / Esser, L. / Singh, S.K. / Maurizi, M.R. / Xia, D.
History
DepositionAug 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-Dependent clp Protease ATP-Binding Subunit clp A
B: Protein yljA


Theoretical massNumber of molelcules
Total (without water)28,2362
Polymers28,2362
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-11 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.249, 91.249, 198.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ATP-Dependent clp Protease ATP-Binding Subunit clp A


Mass: 16043.073 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD-yljA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P0ABH9
#2: Protein Protein yljA


Mass: 12193.038 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pFG42 / Production host: Escherichia coli (E. coli) / Strain (production host): SG22176 / References: UniProt: P0A8Q6

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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

Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.1 MBis-Tris1reservoirpH6.5
332 %glycerol1reservoir
42 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.072 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 3.3→28 Å / Num. all: 13160 / Num. obs: 13160 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.4 % / Biso Wilson estimate: 96.4 Å2 / Rsym value: 0.061 / Net I/σ(I): 30.8
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 14 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 1273 / Rsym value: 0.594 / % possible all: 100
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 28 Å / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.594

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MBU

1mbu


Resolution: 3.3→14.98 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 615032.18 / Data cutoff high rms absF: 615032.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1165 9.4 %RANDOM
Rwork0.257 ---
obs-12331 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.216313 e/Å3
Displacement parametersBiso mean: 84.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.51 Å20 Å20 Å2
2---4.51 Å20 Å2
3---9.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 3.3→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 0 0 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.731.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 3.3→3.5 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.449 167 9.5 %
Rwork0.444 1596 -
obs-1596 82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 12 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.258
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0184
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor Rfree: 0.442 / Rfactor Rwork: 0.571

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