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- PDB-1r6q: ClpNS with fragments -

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Basic information

Entry
Database: PDB / ID: 1r6q
TitleClpNS with fragments
Components(ATP-dependent Clp protease ...) x 2
KeywordsCHAPERONE/PROTEIN BINDING / ClpA / AAA+ / N-terminal domain / ClpS / crystal / binding mechanism / CHAPERONE-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


endopeptidase Clp complex / molecular function inhibitor activity / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / 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 / protein quality control for misfolded or incompletely synthesized proteins / ATP-dependent peptidase activity / 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 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 / 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 / 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 / FOURIER SYNTHESIS / Resolution: 2.35 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 16, 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 1.3Aug 23, 2023Group: 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 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)58,34112
Polymers56,7874
Non-polymers1,5558
Water3,765209
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)29,1716
Polymers28,3932
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-32 kcal/mol
Surface area12680 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)29,1716
Polymers28,3932
Non-polymers7774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-25 kcal/mol
Surface area12890 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8220 Å2
ΔGint-68 kcal/mol
Surface area24230 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
DetailsThe asymmetric unit contains two heterodimeric complexes

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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 ClpA (residues 1-143)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pSK39 / Production host: Escherichia coli (E. coli) / Strain (production host): SG22176 / 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) / Plasmid: pBAD33-clpS / Production host: Escherichia coli (E. coli) / Strain (production host): DH5(alpha) / References: UniProt: P0A8Q6

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Non-polymers , 4 types, 217 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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-Y1 / YTTRIUM ION


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


Mass: 18.015 Da / Num. of mol.: 209 / 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: 4.11 Å3/Da / Density % sol: 70.09 %

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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 / Details: mirrors
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0093 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 39975 / Num. obs: 39975 / % possible obs: 0.999 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 32.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 4.8 / Num. unique all: 3928 / Rsym value: 0.435 / % possible all: 1

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Processing

Software
NameVersionClassification
REFMAC5refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MBU

1mbu


Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.376 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.189 / ESU R Free: 0.17 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22308 819 2.1 %RANDOM
Rwork0.19012 ---
all0.1908 39036 --
obs0.1908 39036 99.98 %-
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: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.13 Å20 Å2
2--0.27 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 74 209 4047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213910
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.9765303
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3123465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55915697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1710.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.31801
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.5299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.371
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.3330.82359
X-RAY DIFFRACTIONr_mcangle_it3.4363.83806
X-RAY DIFFRACTIONr_scbond_it6.01631551
X-RAY DIFFRACTIONr_scangle_it8.3294.51497
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.222 55
Rwork0.207 2796
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)
15.43560.13741.48094.16191.41834.36240.1152-0.55920.06030.427-0.1027-0.1940.1316-0.3561-0.01250.1837-0.01630.02560.28070.03980.072647.92226.49417.7827
24.92350.19981.40483.64290.55475.07810.15120.0279-0.0817-0.0288-0.1159-0.35920.1227-0.1578-0.03520.14140.03460.02980.17350.02310.112349.328623.95516.0318
35.33890.34810.05252.28820.93862.20030.16150.81260.0138-0.3395-0.0647-0.1571-0.07960.1571-0.09680.20930.08120.00420.30960.09650.09399.15459.303714.3173
46.5365-1.4601-0.35875.44360.7692.8280.13430.1064-0.10860.1513-0.1358-0.20540.0910.0530.00150.20520.0276-0.02620.10370.03590.01895.980659.055625.929
55.69073.6296-0.17436.23910.22242.30880.2762-0.2491-0.49180.2019-0.1017-0.462-0.03640.1989-0.17450.1440.0624-0.02850.24270.03060.215173.877635.151614.6537
64.2112-2.85730.69983.5169-0.58371.7451-0.10290.02990.349-0.05160.0925-0.2262-0.1035-0.00170.01030.1029-0.0399-0.03370.19260.01550.120931.186146.196825.3319
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 - 14273 - 142
5X-RAY DIFFRACTION5CC20 - 10620 - 106
6X-RAY DIFFRACTION6DD21 - 10621 - 106

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