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- PDB-4lj4: ClpB NBD2 from T. thermophilus, nucleotide-free -

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Basic information

Entry
Database: PDB / ID: 4lj4
TitleClpB NBD2 from T. thermophilus, nucleotide-free
ComponentsChaperone protein ClpB
KeywordsCHAPERONE / AAA+ protein / nucleotide binding domain / molecular chaperone / disaggregase
Function / homology
Function and homology information


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 repeat (R) N-terminal domain / : / 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 repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Helicase, Ruva Protein; domain 3 - #60 / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsZeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor
Authors: Zeymer, C. / Barends, T.R.M. / Werbeck, N.D. / Schlichting, I. / Reinstein, J.
History
DepositionJul 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _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: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4532
Polymers38,3581
Non-polymers951
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)74.500, 74.500, 118.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsTHE FULL PROTEIN FORMS A RANGE OF OLIGOMERS, AND THIS DOMAIN FORMS DIMERS IN SOLUTION UNDER CERTAIN CIRCUMSTANCES.

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Components

#1: Protein Chaperone protein ClpB


Mass: 38358.000 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain 2, UNP residues 520-854
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: clpB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: Q9RA63
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4

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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: 2.47 Å3/Da / Density % sol: 50.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium citrate, 0.1M HEPES/NaOH, 20% isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9495 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 25, 2005
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9495 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 9176 / Num. obs: 9176 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.074
Reflection shellResolution: 2.8→3 Å / Rmerge(I) obs: 0.534 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
CNSrefinement
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→19.68 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.851 / SU B: 35.56 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R: 1.102 / ESU R Free: 0.474 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30786 457 5 %RANDOM
Rwork0.25355 ---
all0.25619 8700 --
obs0.25619 8700 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.341 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.04 Å20 Å2
2--2.07 Å20 Å2
3----3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2531 0 5 0 2536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222576
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9843482
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4575316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.03222.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.32515467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6171530
X-RAY DIFFRACTIONr_chiral_restr0.0630.2401
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021929
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.21135
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21755
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 34 -
Rwork0.331 656 -
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)
14.8836-1.71070.57385.8366-1.32817.4986-0.05-0.09240.4681-0.6583-0.1123-0.4245-0.76210.29260.16230.0195-0.1240.1063-0.2318-0.0550.0508120.766-5.652-48.293
27.8202-2.07125.812.93-5.196411.8377-0.6966-0.96840.84431.24010.5485-1.0623-0.60710.65480.1481-0.1095-0.0382-0.01720.3413-0.12160.2259135.628-11.95-28.13
31.5507-0.7703-1.177.99955.0629.7686-0.26730.1237-0.72180.4905-0.18430.64491.0143-0.75230.4515-0.1086-0.07890.17260.06460.05440.322125.192-39.225-49.309
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A550 - 710
2X-RAY DIFFRACTION1A741 - 755
3X-RAY DIFFRACTION2A711 - 740
4X-RAY DIFFRACTION3A756 - 849

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