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- PDB-4hse: Crystal structure of ClpB NBD1 in complex with guanidinium chlori... -

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Basic information

Entry
Database: PDB / ID: 4hse
TitleCrystal structure of ClpB NBD1 in complex with guanidinium chloride and ADP
ComponentsChaperone protein ClpB
KeywordsCHAPERONE / nucleotide binding domain / AAA+ protein / molecular chaperone
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 / 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 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GUANIDINE / Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZeymer, C. / Werbeck, N.D. / Schlichting, I. / Reinstein, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The molecular mechanism of hsp100 chaperone inhibition by the prion curing agent guanidinium chloride.
Authors: Zeymer, C. / Werbeck, N.D. / Schlichting, I. / Reinstein, J.
History
DepositionOct 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Sep 20, 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

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Assembly

Deposited unit
A: Chaperone protein ClpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5654
Polymers45,0431
Non-polymers5223
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.990, 60.990, 213.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Chaperone protein ClpB


Mass: 45043.410 Da / Num. of mol.: 1 / Fragment: ClpB NBD1-M (141-534)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: clpB, TTHA1487 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q9RA63
#2: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.55 Å3/Da / Density % sol: 51.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Tris/HCl pH 7.5, 1.0 M LiCl, 18 (w/v) % PEG 6000, 10 mM MgCl2, 10 mM GdmCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9785 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2012
RadiationMonochromator: DOUBLE CRYSTAL SAGITALLY FOCUSING SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 24236 / Num. obs: 24236 / % possible obs: 99.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 19.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2926 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QVR residues 141-534

1qvr


Resolution: 2.2→47.36 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.583 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26631 1207 5 %RANDOM
Rwork0.22536 ---
obs0.22742 23027 100 %-
all-23027 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.543 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2946 0 32 86 3064
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223041
X-RAY DIFFRACTIONr_angle_refined_deg1.1892.014101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.795376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.10223.529153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.01115599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8661540
X-RAY DIFFRACTIONr_chiral_restr0.0780.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212257
X-RAY DIFFRACTIONr_mcbond_it0.4591.51849
X-RAY DIFFRACTIONr_mcangle_it0.92322969
X-RAY DIFFRACTIONr_scbond_it1.6631192
X-RAY DIFFRACTIONr_scangle_it2.954.51127
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 87 -
Rwork0.258 1652 -
obs-1652 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)
12.3009-1.2189-0.55021.78560.65431.479-0.1019-0.0232-0.2020.23530.04450.2932-0.1185-0.18450.05740.07130.02650.04330.21220.05350.05840.356316.5053-14.8097
22.5917-0.91350.42082.1456-0.92721.243-0.0944-0.0216-0.30890.19-0.0097-0.32360.04250.17850.10410.0629-0.0179-0.03130.35310.0480.204835.39758.057-24.5659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A151 - 395
2X-RAY DIFFRACTION2A396 - 532

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