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- PDB-1mbx: CRYSTAL STRUCTURE ANALYSIS OF ClpSN WITH TRANSITION METAL ION BOUND -

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Basic information

Entry
Database: PDB / ID: 1mbx
TitleCRYSTAL STRUCTURE ANALYSIS OF ClpSN WITH TRANSITION METAL ION BOUND
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 / cytoplasm / cytosol
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
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)58,40615
Polymers56,4724
Non-polymers1,93311
Water3,315184
1
A: ATP-Dependent clp Protease ATP-Binding Subunit clp A
C: Protein yljA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9906
Polymers28,2362
Non-polymers7544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-53 kcal/mol
Surface area12620 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)29,4169
Polymers28,2362
Non-polymers1,1797
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-66 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.436, 87.436, 212.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe asymmetric unit contains two heterodimers of ClpSN

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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 genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pBAD33-yljA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: P0ABH9
#2: Protein Protein yljA


Mass: 12193.038 Da / Num. of mol.: 2
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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Non-polymers , 5 types, 195 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-YBT / BIS-(2-HYDROXYETHYL)AMINO-TRIS(HYDROXYMETHYL)METHANE YTTRIUM


Mass: 298.146 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H19NO5Y
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: glycerol, bis-tris , yttrium chloride, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 21K
Crystal grow
*PLUS
pH: 6.5
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: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 26, 2002 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 48936 / Num. obs: 48936 / % possible obs: 92.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 39.2 Å2 / Rsym value: 0.046 / Net I/σ(I): 46.1
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.4 / Num. unique all: 2313 / Rsym value: 0.679 / % possible all: 48.4
Reflection
*PLUS
Highest resolution: 2.25 Å / Lowest resolution: 50 Å / Num. obs: 45812 / % possible obs: 95.9 % / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 69.9 % / Rmerge(I) obs: 0.638

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Processing

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

1mbu


Resolution: 2.25→19.54 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 511609.52 / Data cutoff high rms absF: 511609.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 4404 10 %RANDOM
Rwork0.208 ---
all-43733 --
obs-43733 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8654 Å2 / ksol: 0.347116 e/Å3
Displacement parametersBiso mean: 48.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å21.99 Å20 Å2
2---1.84 Å20 Å2
3---3.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3631 0 96 184 3911
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it3.792.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 569 9.3 %
Rwork0.354 9247 -
obs-5631 71 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3YBT.PARYBT.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
X-RAY DIFFRACTION5ION.PARION.TOP
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_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.08
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / Rfactor Rwork: 0.351

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