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- PDB-4fct: Crystal structure of the C-terminal domain of ClpB -

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Basic information

Entry
Database: PDB / ID: 4fct
TitleCrystal structure of the C-terminal domain of ClpB
ComponentsChaperone protein ClpB
KeywordsCHAPERONE / AAA domain
Function / homology
Function and homology information


protein unfolding / cellular response to heat / protein refolding / ATP hydrolysis activity / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Chaperonin ClpB / 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 ...Chaperonin ClpB / 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 / Clp, N-terminal domain superfamily / Helicase, Ruva Protein; domain 3 - #60 / 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 / Helicase, Ruva Protein; domain 3 / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsBiter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis for intersubunit signaling in a protein disaggregating machine.
Authors: Biter, A.B. / Lee, S. / Sung, N. / Tsai, F.T.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chaperone protein ClpB


Theoretical massNumber of molelcules
Total (without water)34,9311
Polymers34,9311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.220, 56.220, 198.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Chaperone protein ClpB


Mass: 34931.223 Da / Num. of mol.: 1 / Fragment: UNP residues 545-852
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: clpB, TTHA1487 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL CodonPlus / References: UniProt: Q9RA63

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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: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: ammonium sulfate, PEG 3350, 1,6-hexanediol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 4→30 Å / Num. obs: 2925

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4→27.83 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 1 / SU B: 225.095 / SU ML: 1.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 231 7.9 %RANDOM
Rwork0.2855 ---
obs0.2862 2925 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 427.57 Å2 / Biso mean: 240.3191 Å2 / Biso min: 150 Å2
Baniso -1Baniso -2Baniso -3
1-13.07 Å26.53 Å20 Å2
2--13.07 Å20 Å2
3----19.6 Å2
Refinement stepCycle: LAST / Resolution: 4→27.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2348 0 0 0 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222385
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.9873219
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6225290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31522.65117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39215443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2011531
X-RAY DIFFRACTIONr_chiral_restr0.0580.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211790
LS refinement shellResolution: 4→4.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 18 -
Rwork0.384 180 -
all-198 -
obs--100 %
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)
126.8443-8.9529-16.5492-2.181618.804758.12071.49632.76731.89520.9636-0.8558-1.11-0.3321-4.5267-0.64050.23750.1784-0.4231.0120.27510.9551-18.080530.548626.1574
212.01964.657-1.63480.7192-6.638428.9741-0.98120.768-0.2738-0.75951.28250.0885-0.73670.4859-0.30130.2807-0.11390.02010.44650.32340.7416-11.100433.887531.4789
319.07164.8872-12.01985.832-29.071481.77572.4317-2.3565-5.0995-0.3684-4.07220.7315-3.76831.03141.64061.85580.9037-0.3510.10650.51861.0558-14.698344.402934.3705
416.50562.62013.60426.6636-0.60897.8080.4613-0.41250.57240.79-0.0441-0.1849-0.2370.1143-0.41710.07160.5783-0.01290.69210.23410.3112-24.368210.751517.5252
5-10.103264.8683-22.436712.92940.179821.9660.1893-1.0508-2.5032-0.46761.0998-6.43913.79591.7707-1.28910.25350.6715-0.78482.03771.43011.2571-4.1732-2.947422.2309
68.83114.7375-6.35396.9882-3.723218.63040.14710.1257-0.6963-0.72240.5959-0.82481.95730.9815-0.74290.51240.4584-0.28040.645-0.01950.5641-14.06750.540916.374
7-3.324414.10546.1202-0.975423.361312.7935-1.037-1.1105-0.9694-3.47751.1592-0.9016-1.26353.0465-0.12210.96030.44650.24741.44810.46840.0095-13.31299.2592.3526
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A757 - 779
2X-RAY DIFFRACTION2A780 - 830
3X-RAY DIFFRACTION3A831 - 850
4X-RAY DIFFRACTION4A545 - 622
5X-RAY DIFFRACTION5A623 - 651
6X-RAY DIFFRACTION6A652 - 722
7X-RAY DIFFRACTION7A723 - 756

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