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- PDB-1mbu: Crystal Structure Analysis of ClpSN heterodimer -

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Basic information

Entry
Database: PDB / ID: 1mbu
TitleCrystal Structure Analysis of ClpSN heterodimer
Components
  • ATP-Dependent clp Protease ATP-Binding Subunit clp A
  • Protein yljA
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / molecular function inhibitor activity / protein unfolding / protein catabolic process / cellular response to heat / response to heat / protein-folding chaperone binding / response to oxidative stress ...endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / molecular function inhibitor activity / protein unfolding / protein catabolic process / cellular response to heat / response to heat / protein-folding chaperone binding / 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 adaptor protein ClpS / Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / 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 adaptor protein ClpS / Double Clp-N motif / Clp, N-terminal domain / ATP-dependent Clp protease ATP-binding subunit ClpA / 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 amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-YBT / 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 / MIR / Resolution: 2.3 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 the 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: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: ATP-Dependent clp Protease ATP-Binding Subunit clp A
C: Protein yljA
D: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,92012
Polymers56,4724
Non-polymers1,4488
Water2,720151
1
A: ATP-Dependent clp Protease ATP-Binding Subunit clp A
C: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6264
Polymers28,2362
Non-polymers3902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-16 kcal/mol
Surface area12320 Å2
MethodPISA
2
B: ATP-Dependent clp Protease ATP-Binding Subunit clp A
D: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2948
Polymers28,2362
Non-polymers1,0576
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-37 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.913, 87.913, 209.420
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 16043.073 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0ABH9
#2: Protein Protein yljA


Mass: 12193.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P0A8Q6

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Non-polymers , 4 types, 159 molecules

#3: Chemical
ChemComp-YBT / BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANE YTTRIUM


Mass: 298.146 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H19NO5Y
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 4.14 Å3/Da / Density % sol: 70.26 %
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 Mbis-Tris1reservoirpH6.5
232 %glycerol1reservoir
310-15 mMyttrium chloride1reservoir
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.0093 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 7, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 42650 / Num. obs: 42650 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.31 % / Biso Wilson estimate: 31.6 Å2 / Rsym value: 0.065 / Net I/σ(I): 32.4
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2785 / Rsym value: 0.621 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.579

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MIR / Resolution: 2.3→19.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 205889.83 / Data cutoff high rms absF: 205889.83 / 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
Rfree0.251 4223 10.2 %RANDOM
Rwork0.217 ---
all-42465 --
obs-41554 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.3545 Å2 / ksol: 0.342738 e/Å3
Displacement parametersBiso mean: 43.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.19 Å24.15 Å20 Å2
2--1.19 Å20 Å2
3----2.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 74 151 3851
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.332
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.442.5
Refine LS restraints NCSNCS model details: RESTRAINT
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.29 629 9.5 %
Rwork0.265 5994 -
obs-6623 94.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMYBT.TOP
X-RAY DIFFRACTION3ION.PARGOL.TOP
X-RAY DIFFRACTION4YBT.PARION.TOP
X-RAY DIFFRACTION5GOL.PAR
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0116
X-RAY DIFFRACTIONc_angle_deg1.46
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / Rfactor Rwork: 0.351

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