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- PDB-4lj5: ClpB NBD2 from T. thermophilus in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 4lj5
TitleClpB NBD2 from T. thermophilus in complex with ADP
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
ADENOSINE-5'-DIPHOSPHATE / Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 8, 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_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)38,7852
Polymers38,3581
Non-polymers4271
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.060, 76.060, 120.540
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M sodium citrate, 0.1M HEPES/NaOH, 20% isopropanol, 2mM ADP, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.01096 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2003
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.01096 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 17302 / Num. obs: 17302 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.085 / Net I/σ(I): 10.12
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.774 / Mean I/σ(I) obs: 2.12 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNSrefinement
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QVR

1qvr


Resolution: 2.4→19.27 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.914 / SU B: 19.264 / SU ML: 0.246 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.466 / ESU R Free: 0.283 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27211 762 5 %RANDOM
Rwork0.23522 ---
all0.23706 14464 --
obs0.23706 14464 99.98 %-
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: 65.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20.38 Å20 Å2
2--0.75 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 27 58 2620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222607
X-RAY DIFFRACTIONr_bond_other_d0.0010.022519
X-RAY DIFFRACTIONr_angle_refined_deg0.9222.0013531
X-RAY DIFFRACTIONr_angle_other_deg0.71935815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.35317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50722.917120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50915468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9241530
X-RAY DIFFRACTIONr_chiral_restr0.0480.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02531
X-RAY DIFFRACTIONr_nbd_refined0.160.2506
X-RAY DIFFRACTIONr_nbd_other0.1510.22455
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21238
X-RAY DIFFRACTIONr_nbtor_other0.0780.21490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0870.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.22
X-RAY DIFFRACTIONr_mcbond_it0.1721.52075
X-RAY DIFFRACTIONr_mcbond_other0.0211.5646
X-RAY DIFFRACTIONr_mcangle_it0.19222576
X-RAY DIFFRACTIONr_scbond_it0.36331139
X-RAY DIFFRACTIONr_scangle_it0.6034.5955
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 56 -
Rwork0.292 1071 -
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)
12.97320.8582-0.80755.5028-0.76715.4135-0.143-0.1064-0.33620.6267-0.2029-0.08720.32610.29210.3459-0.20630.0285-0.0144-0.3925-0.0214-0.170347.8465.65748.872
28.00711.9258-3.493123.0496-9.11327.7813-0.02311.4013-0.3608-1.674-0.466-1.5260.21390.6480.4891-0.1171-0.02560.11210.3392-0.0342-0.068762.37913.0827.954
33.47752.15072.26967.38764.6815.6292-0.4272-0.10741.2735-0.6561-0.11880.7805-0.631-0.40590.546-0.2336-0.0079-0.2388-0.23980.08620.264751.28740.01950.491
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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