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- PDB-4qyx: Crystal structure of YDR533Cp -

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Basic information

Entry
Database: PDB / ID: 4qyx
TitleCrystal structure of YDR533Cp
ComponentsProbable chaperone protein HSP31
KeywordsHYDROLASE / alpha-beta sandwich / DJ-1/ThiJ/PfpI superfamily / glyoxalase III
Function / homology
Function and homology information


D-lactate dehydratase / glyoxalase III activity / : / cellular response to nutrient levels / protein folding chaperone / P-body / cytoplasmic stress granule / protein folding / cellular response to oxidative stress / cytoplasm
Similarity search - Function
: / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutathione-independent glyoxalase HSP31
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.69 Å
AuthorsWilson, M.A. / Amour, S.T. / Collins, J.L. / Ringe, D. / Petsko, G.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The 1.8-A resolution crystal structure of YDR533Cp from Saccharomyces cerevisiae: A member of the DJ-1/ThiJ/PfpI superfamily.
Authors: Wilson, M.A. / Amour, S.T. / Collins, J.L. / Ringe, D. / Petsko, G.A.
History
DepositionJul 26, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionAug 6, 2014ID: 1RW7
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable chaperone protein HSP31


Theoretical massNumber of molelcules
Total (without water)26,7571
Polymers26,7571
Non-polymers00
Water3,207178
1
A: Probable chaperone protein HSP31

A: Probable chaperone protein HSP31


Theoretical massNumber of molelcules
Total (without water)53,5142
Polymers53,5142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.283, 68.786, 137.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable chaperone protein HSP31 / Heat shock protein 31


Mass: 26757.002 Da / Num. of mol.: 1 / Mutation: D233V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D9719.36, HSP31, YDR533C / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04432, Hydrolases; Glycosylases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.04 Å3/Da / Density % sol: 39.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 35-40% PEG 2000, 100 mM SODIUM ACETATE, 200 mM AMMONIUM ACETATE, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→68.6 Å / Num. all: 24700 / Num. obs: 24700 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rsym value: 0.076 / Net I/σ(I): 29.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 2409 / Rsym value: 0.697 / % possible all: 98.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.8.0073refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.69→68.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.84 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23334 2488 10.1 %RANDOM
Rwork0.19228 ---
all0.19637 24664 --
obs0.19637 24664 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.947 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.69→68.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 0 178 1976
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191847
X-RAY DIFFRACTIONr_bond_other_d0.0010.021740
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9532505
X-RAY DIFFRACTIONr_angle_other_deg0.85534025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7795236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29925.2580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.849154
X-RAY DIFFRACTIONr_chiral_restr0.0910.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212108
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02406
X-RAY DIFFRACTIONr_mcbond_it0.6591.049944
X-RAY DIFFRACTIONr_mcbond_other0.6481.047943
X-RAY DIFFRACTIONr_mcangle_it1.0731.5681180
X-RAY DIFFRACTIONr_mcangle_other1.0721.571181
X-RAY DIFFRACTIONr_scbond_it0.8531.172903
X-RAY DIFFRACTIONr_scbond_other0.8531.174904
X-RAY DIFFRACTIONr_scangle_other1.3691.7061326
X-RAY DIFFRACTIONr_long_range_B_refined5.5839.7252255
X-RAY DIFFRACTIONr_long_range_B_other5.5159.1722188
LS refinement shellResolution: 1.693→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 171 -
Rwork0.276 1510 -
obs-1681 92.11 %
Refinement TLS params.Method: refined / Origin x: 4.3172 Å / Origin y: 4.4886 Å / Origin z: 16.9708 Å
111213212223313233
T0.2405 Å20.0651 Å20.0709 Å2-0.0278 Å20.0174 Å2--0.0331 Å2
L1.1078 °21.1133 °2-0.2439 °2-3.688 °2-1.0565 °2--1.5749 °2
S-0.037 Å °0.0291 Å °-0.0859 Å °-0.7553 Å °-0.1281 Å °-0.3266 Å °0.2084 Å °0.1057 Å °0.165 Å °

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