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- PDB-1r6o: ATP-dependent Clp protease ATP-binding subunit clpA/ATP-dependent... -

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Basic information

Entry
Database: PDB / ID: 1r6o
TitleATP-dependent Clp protease ATP-binding subunit clpA/ATP-dependent Clp protease adaptor protein clpS
Components(ATP-dependent Clp protease ...) x 2
KeywordsHYDROLASE / ClpA / AAA+ / N-terminal domain / ClpS / crystal / binding mechanism
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
YTTRIUM ION / 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: 2.25 Å
AuthorsXia, D. / Maurizi, M.R. / Guo, F. / Singh, S.K. / Esser, L.
CitationJournal: J.Struct.Biol. / Year: 2004
Title: Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone
Authors: Xia, D. / Esser, L. / Singh, S.K. / Guo, F. / Maurizi, M.R.
History
DepositionOct 15, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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 clpA
B: ATP-dependent Clp protease ATP-binding subunit clpA
C: ATP-dependent Clp protease adaptor protein clpS
D: ATP-dependent Clp protease adaptor protein clpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,60016
Polymers56,7874
Non-polymers1,81312
Water4,990277
1
A: ATP-dependent Clp protease ATP-binding subunit clpA
C: ATP-dependent Clp protease adaptor protein clpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1476
Polymers28,3932
Non-polymers7544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-61 kcal/mol
Surface area12700 Å2
MethodPISA
2
B: ATP-dependent Clp protease ATP-binding subunit clpA
D: ATP-dependent Clp protease adaptor protein clpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,45210
Polymers28,3932
Non-polymers1,0598
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-84 kcal/mol
Surface area12760 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-158 kcal/mol
Surface area24100 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

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Components

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ATP-dependent Clp protease ... , 2 types, 4 molecules ABCD

#1: Protein ATP-dependent Clp protease ATP-binding subunit clpA


Mass: 16200.268 Da / Num. of mol.: 2 / Fragment: N-Terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CLPA, LOPD, B0882, C1019, Z1119, ECS0968 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABH9
#2: Protein ATP-dependent Clp protease adaptor protein clpS


Mass: 12193.038 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CLPS, B0881, C1018, Z1118, ECS0967, SF0841, S0881 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q6

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Non-polymers , 6 types, 289 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.: 4 / Source method: obtained synthetically / Formula: C8H19NO5Y
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-Y1 / YTTRIUM ION / Yttrium


Mass: 88.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Y
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 70.28 %
Crystal growTemperature: 294 K
Details: Drop: 0.02M Tris HCl (pH 8.5), 2mM ZnCl2, 10% (w/v) glycerol; Precipitant: 0.1M bis-tris (pH 6.5), 32% (w/v) glycerol, 0.01-0.015M yttrium chloride, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 1.2823 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 25, 2002 / Details: mirrors
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 45504 / Num. obs: 45504 / % possible obs: 0.991 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 27.7
Reflection shellResolution: 2.25→2.3 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.75 / Num. unique all: 3745 / Rsym value: 0.68 / % possible all: 0.94

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.25→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.067 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.144 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.20546 922 2.1 %RANDOM
Rwork0.18991 ---
all0.19022 43921 --
obs0.19022 43921 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.269 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0.28 Å20 Å2
2---0.57 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3765 0 83 277 4125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0213916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.9785305
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3463463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20515696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1670.2613
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.31866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.5333
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1450.57
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.362
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.515
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.2820.82359
X-RAY DIFFRACTIONr_mcangle_it3.2243.83801
X-RAY DIFFRACTIONr_scbond_it5.76931557
X-RAY DIFFRACTIONr_scangle_it8.1594.51504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 61
Rwork0.324 2697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.5977-0.12940.91462.9341.10724.51710.1185-0.66410.18160.448-0.1022-0.18950.0537-0.2733-0.01630.1917-0.0214-0.00780.25210.01660.155347.281326.731617.2972
25.1906-0.28111.12492.6734-0.31634.18750.1386-0.037-0.1491-0.0376-0.0542-0.31610.1964-0.0936-0.08450.13380.01460.01170.15140.00890.163148.984524.06695.6635
36.37430.04850.44552.91480.69392.83830.16870.73420.0219-0.2308-0.0351-0.1111-0.13630.0694-0.13360.18250.0490.01290.21030.06410.03698.876459.346415.0489
46.5502-0.9784-0.48855.28290.8942.99260.0904-0.2532-0.2090.2657-0.061-0.20610.1090.02-0.02940.21850.0255-0.01540.11470.05020.02536.110558.514726.6516
54.73923.5040.10836.21510.20832.23070.2629-0.1609-0.54280.1901-0.2078-0.5190.02980.1485-0.0550.15440.0244-0.03410.24210.04530.244373.415535.066614.8278
64.5795-1.91180.45423.0062-0.21991.950.0219-0.14370.16620.04130.0401-0.34-0.03660.0556-0.06190.1204-0.0217-0.0560.17150.01280.136431.070846.113525.3066
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 721 - 72
2X-RAY DIFFRACTION2AA73 - 14273 - 142
3X-RAY DIFFRACTION3BB1 - 721 - 72
4X-RAY DIFFRACTION4BB73 - 14173 - 141
5X-RAY DIFFRACTION5CC20 - 10620 - 106
6X-RAY DIFFRACTION6DD21 - 10621 - 106

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