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- PDB-4lja: ClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and g... -

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Basic information

Entry
Database: PDB / ID: 4lja
TitleClpB NBD2 R621Q from T. thermophilus in complex with AMPPCP and guanidinium chloride
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 amino terminal domain, pathogenicity island component / : / 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 / Clp repeat (R) domain profile. / 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 / Helicase, Ruva Protein; domain 3 - #60 / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANIDINE / Chaperone protein ClpB
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
Revision 1.3Nov 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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)38,9184
Polymers38,3291
Non-polymers5893
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 74.800, 119.500
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: 38328.934 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain 2, UNP residues 520-854 / Mutation: R621Q
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-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris/HCl, 15% isopropanol, 10mM magnesium chloride, 2mM AMPPCP, 100mM guanidinium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.912 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2013
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.912 Å / Relative weight: 1
ReflectionResolution: 2→44 Å / Num. all: 25581 / Num. obs: 25581 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.1
Reflection shellResolution: 2→2.1 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 3 / Num. unique all: 3479 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LJ5

4lj5


Resolution: 2→43.92 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.218 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26343 1256 4.9 %RANDOM
Rwork0.2172 ---
all0.21935 24325 --
obs0.21935 24325 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.841 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2→43.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 36 77 2663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222634
X-RAY DIFFRACTIONr_angle_refined_deg1.25623569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.095320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56723.065124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48615472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6941530
X-RAY DIFFRACTIONr_chiral_restr0.0790.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211968
X-RAY DIFFRACTIONr_mcbond_it0.4891.51602
X-RAY DIFFRACTIONr_mcangle_it0.92422588
X-RAY DIFFRACTIONr_scbond_it1.61331032
X-RAY DIFFRACTIONr_scangle_it2.7664.5980
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 91 -
Rwork0.275 1797 -
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)
14.3668-0.358-0.06963.0169-0.08472.63640.11490.50460.0054-0.2927-0.2983-0.37840.09490.10620.18330.07680.06660.02210.09950.02880.06778.982226.5167-9.1661
214.0622-3.9353-3.6155.30660.73877.0046-0.4709-0.8545-0.79340.82130.17580.35510.4917-0.43960.29510.2955-0.06450.01760.19750.03150.064-4.257117.851311.7143
35.2864-1.02193.73082.8926-0.89834.1198-0.3449-0.20970.61650.01980.11310.4526-0.4931-0.21350.23180.11090.0532-0.04150.1242-0.09360.2874-21.845640.5552-10.5264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A550 - 709
2X-RAY DIFFRACTION1A741 - 755
3X-RAY DIFFRACTION2A710 - 740
4X-RAY DIFFRACTION3A756 - 849

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