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- PDB-4j7z: Thermus thermophilus DNAJ J- and G/F-DOMAINS -

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Basic information

Entry
Database: PDB / ID: 4j7z
TitleThermus thermophilus DNAJ J- and G/F-DOMAINS
ComponentsChaperone protein DnaJ 2
KeywordsCHAPERONE / J-DOMAIN / POLYPROLINE-II HELIX / DNA REPLICATION / STRESS RESPONSE
Function / homology
Function and homology information


unfolded protein binding / protein folding / DNA replication / cytoplasm
Similarity search - Function
DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily ...DnaJ domain / HSP40/DnaJ peptide-binding / Chaperone DnaJ, C-terminal / DnaJ C terminal domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chaperone protein DnaJ 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / EPR / SYNCHROTRON / RIPAS / Resolution: 1.64 Å
AuthorsBarends, T.R.M. / Brosi, R.W. / Steinmetz, A. / Scherer, A. / Hartmann, E. / Eschenbach, J. / Lorenz, T. / Seidel, R. / Shoeman, R. / Zimmermann, S. ...Barends, T.R.M. / Brosi, R.W. / Steinmetz, A. / Scherer, A. / Hartmann, E. / Eschenbach, J. / Lorenz, T. / Seidel, R. / Shoeman, R. / Zimmermann, S. / Bittl, R. / Schlichting, I. / Reinstein, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ.
Authors: Barends, T.R. / Brosi, R.W. / Steinmetz, A. / Scherer, A. / Hartmann, E. / Eschenbach, J. / Lorenz, T. / Seidel, R. / Shoeman, R.L. / Zimmermann, S. / Bittl, R. / Schlichting, I. / Reinstein, J.
History
DepositionFeb 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 DnaJ 2
B: Chaperone protein DnaJ 2
C: Chaperone protein DnaJ 2
D: Chaperone protein DnaJ 2
E: Chaperone protein DnaJ 2
F: Chaperone protein DnaJ 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7989
Polymers77,5226
Non-polymers2763
Water6,161342
1
A: Chaperone protein DnaJ 2


Theoretical massNumber of molelcules
Total (without water)12,9201
Polymers12,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Chaperone protein DnaJ 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0122
Polymers12,9201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Chaperone protein DnaJ 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0122
Polymers12,9201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Chaperone protein DnaJ 2


Theoretical massNumber of molelcules
Total (without water)12,9201
Polymers12,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Chaperone protein DnaJ 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0122
Polymers12,9201
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Chaperone protein DnaJ 2


Theoretical massNumber of molelcules
Total (without water)12,9201
Polymers12,9201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.990, 85.990, 72.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Chaperone protein DnaJ 2 /


Mass: 12920.283 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 2-114 / Mutation: L57(MSE), I142(MSE), L173(MSE), L226(MSE), K231G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: dnaJ2, TTHA1489 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56237
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION
EPR1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.95 %
Crystal growMethod: vapor diffusion, hanging drop
Details: PEG1500 15%, 0.1 M STRONTIUM CHLORIDE , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9536
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2006
Details: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR, DYNAMICALLY BENDABLE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9536 Å / Relative weight: 1
ReflectionResolution: 1.64→40 Å / Num. obs: 72046 / % possible obs: 97.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 12.5
Reflection shellResolution: 1.64→1.7 Å / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.8 / % possible all: 94.9

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: RIPAS / Resolution: 1.64→37.24 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 3545 4.9 %THIN RESOLUTION SHELLS
Rwork0.214 ---
obs0.216 68483 97.8 %-
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: 36.039 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.64→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4918 0 18 342 5278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225088
X-RAY DIFFRACTIONr_bond_other_d00.024351
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.986889
X-RAY DIFFRACTIONr_angle_other_deg3.583310218
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.8985594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.28923.986281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57215799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8881536
X-RAY DIFFRACTIONr_chiral_restr0.0710.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025728
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021096
X-RAY DIFFRACTIONr_nbd_refined0.1970.21140
X-RAY DIFFRACTIONr_nbd_other0.2050.23865
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22579
X-RAY DIFFRACTIONr_nbtor_other0.1020.22263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0630.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.170.2121
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8211.53028
X-RAY DIFFRACTIONr_mcbond_other01.51188
X-RAY DIFFRACTIONr_mcangle_it3.96124886
X-RAY DIFFRACTIONr_scbond_it3.20832060
X-RAY DIFFRACTIONr_scangle_it4.5724.52003
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.68 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 4 -
Rwork0.263 5142 -
obs--94.32 %
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)
12.59680.20390.16763.3595-0.27734.48340.03160.3345-0.3486-0.26590.07110.06460.6554-0.1179-0.1027-0.11350.0043-0.0111-0.0815-0.0626-0.1826-10.87540.97764.074
22.091-0.4040.14621.8559-1.38695.25580.1493-0.05360.04090.1963-0.03150.1652-0.1469-0.436-0.1179-0.155-0.01390.0152-0.1925-0.0234-0.2011-12.73146.83990.73
33.4586-0.1205-0.12732.83990.76517.0120.11870.26570.1786-0.05150.0494-0.2285-0.55570.4324-0.168-0.15670.04290.0233-0.14360.0263-0.1845-30.40169.84883.247
41.7950.0943-0.19043.24921.98438.6027-0.1438-0.1449-0.16820.42060.13940.0410.95180.40660.0044-0.01810.13820.0368-0.16730.049-0.181-33.98564.017109.849
53.39510.4418-2.07950.43140.36764.87940.18760.28970.1175-0.23210.10620.0799-0.7803-0.7803-0.29380.07950.12710.0824-0.06340.0633-0.0921-48.76236.75734.689
63.1463-1.52210.27893.986-0.49665.2887-0.0402-0.1255-0.44340.18040.1166-0.05560.68840.2388-0.0764-0.01310.00510.0757-0.1503-0.0168-0.0555-31.40717.98237.09
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 101
2X-RAY DIFFRACTION2B2 - 101
3X-RAY DIFFRACTION3C2 - 101
4X-RAY DIFFRACTION4D2 - 107
5X-RAY DIFFRACTION5E4 - 101
6X-RAY DIFFRACTION6F2 - 101

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