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- PDB-2qsa: Crystal structure of J-domain of DnaJ homolog dnj-2 precursor fro... -

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Basic information

Entry
Database: PDB / ID: 2qsa
TitleCrystal structure of J-domain of DnaJ homolog dnj-2 precursor from C.elegans.
ComponentsDnaJ homolog dnj-2
KeywordsCHAPERONE / J-domain / hsp40 / APC90001.8 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


protein folding / endoplasmic reticulum membrane
Similarity search - Function
DnaJ homolog subfamily C member 25-like / DnaJ 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 ...DnaJ homolog subfamily C member 25-like / DnaJ 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
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsOsipiuk, J. / Mulligan, R. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of J-domain of DnaJ homolog dnj-2 precursor from C.elegans.
Authors: Osipiuk, J. / Mulligan, R. / Gu, M. / Voisine, C. / Morimoto, R.I. / Joachimiak, A.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DnaJ homolog dnj-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1512
Polymers13,1161
Non-polymers351
Water1,964109
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.148, 81.148, 60.016
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21A-366-

HOH

31A-392-

HOH

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Components

#1: Protein DnaJ homolog dnj-2 / DnaJ domain protein 2


Mass: 13115.672 Da / Num. of mol.: 1 / Fragment: N-terminal J domain: Residues 24-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Strain: Bristol N2 / Gene: dnj-2, B0035.2 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q17433
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M NaCl, 0.1 M Tris buffer pH 7.0, 0.2 M MgCl2, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.68→27.7 Å / Num. all: 16389 / Num. obs: 16389 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 33.7
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 1.94 / Num. unique all: 848 / % possible all: 74.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O37

2o37
PDB Unreleased entry


Resolution: 1.68→27.7 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.196 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.089 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1803 829 5.1 %RANDOM
Rwork0.1631 ---
all0.1639 15558 --
obs0.1639 15558 97.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.524 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.68→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 1 109 981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221037
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.9681429
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0435133
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9224.22571
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0115199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7671511
X-RAY DIFFRACTIONr_chiral_restr0.1220.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02857
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.2490
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2711
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0671.5589
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4962937
X-RAY DIFFRACTIONr_scbond_it2.4513510
X-RAY DIFFRACTIONr_scangle_it3.5214.5472
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 48 -
Rwork0.276 883 -
obs-931 75.81 %
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)
11.19340.82262.87792.91321.62056.9961-0.0691-0.07830.01220.14440.01610.1249-0.15-0.49230.053-0.0120.00320.01110.0388-0.00280.007115.43043.536728.0875
21.2555-0.2178-1.23420.7113-0.56172.10680.0288-0.23380.128-0.00770.0520.0079-0.07730.1681-0.08080.0162-0.03130.00250.0266-0.02880.004924.74885.69222.3509
32.058-3.6799-4.654711.78145.747211.80320.50610.15510.5789-0.06690.3932-0.5226-0.6230.222-0.89930.1098-0.07940.1027-0.0769-0.05370.077227.185914.221315.6258
40.037-0.25940.20651.8232-1.3483.84910.0153-0.00820.03850.08740.0604-0.0507-0.1930.2835-0.07570.0171-0.02280.00780.047-0.0076-0.019331.01792.389412.1195
50.9027-1.1932-0.88757.8179-4.82316.63360.13640.04340.1002-0.1903-0.41670.12410.43840.88750.28040.03610.0767-0.01690.06710.0024-0.042934.5206-8.955416.8597
615.48461.5587.6641.424-14.55829.4832-0.4632-0.0476-0.43641.0172-0.5832-1.35850.98341.03371.04640.30360.1942-0.0053-0.10340.0418-0.065635.0892-17.980223.8775
73.4497-1.45720.73111.30240.29090.67870.0690.1592-0.1910.22880.01850.21740.2469-0.0736-0.08750.11430.03810.022-0.0204-0.0097-0.01928.1307-12.165323.1643
80.5087-0.13971.0050.16430.24754.16230.08660.0409-0.07530.0518-0.02920.10750.09040.0399-0.05740.01730.00250.01370.0208-0.00610.004524.1913-3.806417.9092
93.6246-0.0323-1.62510.44430.71451.83240.01670.11640.1918-0.07650.0532-0.0047-0.0478-0.0654-0.06990.01970.0141-0.0174-0.00610.01940.008814.94756.998217.0171
105.78110.7066-1.24483.0091.21640.9089-0.27720.2268-0.2929-0.12540.2352-0.107-0.1793-0.15090.042-0.0369-0.01110.01590.0476-0.0150.02426.20512.164518.8636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA22 - 322 - 12
2X-RAY DIFFRACTION2AA33 - 4513 - 25
3X-RAY DIFFRACTION3AA46 - 4926 - 29
4X-RAY DIFFRACTION4AA50 - 6130 - 41
5X-RAY DIFFRACTION5AA62 - 6742 - 47
6X-RAY DIFFRACTION6AA68 - 7448 - 54
7X-RAY DIFFRACTION7AA75 - 8255 - 62
8X-RAY DIFFRACTION8AA83 - 8963 - 69
9X-RAY DIFFRACTION9AA90 - 10970 - 89
10X-RAY DIFFRACTION10AA110 - 12290 - 102

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