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- PDB-1lzw: Structural basis of ClpS-mediated switch in ClpA substrate recognition -

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Basic information

Entry
Database: PDB / ID: 1lzw
TitleStructural basis of ClpS-mediated switch in ClpA substrate recognition
Components
  • ATP-dependent clp protease ATP-binding subunit ClpA
  • Protein yljA
KeywordsCHAPERONE / alpha-beta-protein (ClpS) / alpha-protein (ClpA-ND)
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 / MAD / Resolution: 2.5 Å
AuthorsZeth, K. / Ravelli, R.B. / Paal, K. / Cusack, S. / Bukau, B. / Dougan, D.A.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA
Authors: Zeth, K. / Ravelli, R.B. / Paal, K. / Cusack, S. / Bukau, B. / Dougan, D.A.
History
DepositionJun 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein yljA
B: ATP-dependent clp protease ATP-binding subunit ClpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8953
Polymers28,7002
Non-polymers1951
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area12570 Å2
MethodPISA
2
A: Protein yljA
B: ATP-dependent clp protease ATP-binding subunit ClpA
hetero molecules

A: Protein yljA
B: ATP-dependent clp protease ATP-binding subunit ClpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7896
Polymers57,3994
Non-polymers3902
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3980 Å2
ΔGint-59 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.880, 114.590, 38.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-300-

PT

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Components

#1: Protein Protein yljA


Mass: 12125.969 Da / Num. of mol.: 1 / Mutation: H66A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q6
#2: Protein ATP-dependent clp protease ATP-binding subunit ClpA


Mass: 16573.650 Da / Num. of mol.: 1 / Fragment: Residues 1-146
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9
#3: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: 20% iPr, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal grow
*PLUS
Temperature: 278 K / pH: 7.5 / Details: Zeth, K., (2002) Acta Crystallogr., D58, 1207.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
120 mM1dropNaCl
220 mM1dropKCl
310 mMHEPES1droppH7.5
410 mg/mlprotein1drop
520 %2-propanol1reservoir
620 %PEG40001reservoir
70.1 Msodium citrate1reservoirpH5.6
810 mMspermine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 2001 / Details: mirrors
RadiationMonochromator: beam collimation 100 x 100 um monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→19.69 Å / Num. obs: 14343 / % possible obs: 98.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.122 / Net I/σ(I): 17.9
Reflection shellHighest resolution: 2.5 Å / % possible all: 98.6
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 26527 / % possible obs: 98.3 % / Num. measured all: 55297 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 1.52

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.69 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 87059.26 / Data cutoff high rms absF: 87059.26 / 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
Rfree0.267 1435 10 %RANDOM
Rwork0.243 ---
obs0.243 14343 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.8347 Å2 / ksol: 0.354532 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--7.88 Å20 Å20 Å2
2--17.72 Å20 Å2
3----9.83 Å2
Refine analyzeLuzzati coordinate error free: 0.37 Å / Luzzati sigma a free: 0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 1 49 1908
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.721.5
X-RAY DIFFRACTIONc_mcangle_it3.092
X-RAY DIFFRACTIONc_scbond_it2.752
X-RAY DIFFRACTIONc_scangle_it4.082.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 237 10 %
Rwork0.343 2129 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / Num. reflection obs: 14573 / Num. reflection Rfree: 718 / % reflection Rfree: 10 % / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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