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- PDB-1xao: Hsp40-Ydj1 dimerization domain -

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Basic information

Entry
Database: PDB / ID: 1xao
TitleHsp40-Ydj1 dimerization domain
ComponentsMitochondrial protein import protein MAS5Mitochondrion
KeywordsCHAPERONE / Beta sheets
Function / homology
Function and homology information


tRNA import into nucleus / TRC complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to oxygen levels / protein targeting to ER / protein targeting to mitochondrion / 'de novo' protein folding / ERAD pathway / ATPase activator activity / chaperone-mediated protein complex assembly ...tRNA import into nucleus / TRC complex / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to oxygen levels / protein targeting to ER / protein targeting to mitochondrion / 'de novo' protein folding / ERAD pathway / ATPase activator activity / chaperone-mediated protein complex assembly / Hsp70 protein binding / transcription repressor complex / unfolded protein binding / protein transport / protein-folding chaperone binding / response to heat / protein refolding / ubiquitin-dependent protein catabolic process / negative regulation of DNA-templated transcription / perinuclear region of cytoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #310 / DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Heat shock protein DnaJ, cysteine-rich domain superfamily / HSP40/DnaJ peptide-binding ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #310 / DnaJ homolog subfamily A member 1/2-like / Chaperone DnaJ / DnaJ central domain / Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / Urease metallochaperone UreE, N-terminal domain / HSP40/DNAj peptide-binding domain / Heat shock protein DnaJ, cysteine-rich domain superfamily / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Sandwich / Mainly Beta
Similarity search - Domain/homology
Mitochondrial protein import protein MAS5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsWu, Y. / Sha, B.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: The crystal structure of the C-terminal fragment of yeast Hsp40 Ydj1 reveals novel dimerization motif for Hsp40
Authors: Wu, Y. / Li, J. / Jin, Z. / Fu, Z. / Sha, B.
History
DepositionAug 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial protein import protein MAS5
B: Mitochondrial protein import protein MAS5


Theoretical massNumber of molelcules
Total (without water)26,5332
Polymers26,5332
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-51 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.631, 49.631, 210.191
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Mitochondrial protein import protein MAS5 / Mitochondrion / YDJ1


Mass: 13266.318 Da / Num. of mol.: 2 / Fragment: Ydj1 (residues 258-378)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MAS5, YDJ1 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P25491
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.615 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Sodium Chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97936, 0.97947, 0.97242
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 29, 2004 / Details: ID
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979361
20.979471
30.972421
ReflectionResolution: 2.07→27.16 Å / Num. all: 15669 / Num. obs: 15669 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 18.2 Å2
Reflection shellResolution: 2.07→2.13 Å / % possible all: 67.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.07→27.16 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1656796.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1230 7.8 %RANDOM
Rwork0.219 ---
all0.219 15669 --
obs0.219 15669 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.7505 Å2 / ksol: 0.340822 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.23 Å24.82 Å20 Å2
2--7.23 Å20 Å2
3----14.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.07→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 0 232 2014
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.07→2.13 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 47 9 %
Rwork0.26 475 -
obs-475 16 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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