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- PDB-1qvw: Crystal structure of the S. cerevisiae YDR533c protein -

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Basic information

Entry
Database: PDB / ID: 1qvw
TitleCrystal structure of the S. cerevisiae YDR533c protein
ComponentsYDR533c protein
Keywordsstructural genomics / unknown function / alpha/beta hydrolase fold / catalytic triad / heat shock protein
Function / homology
Function and homology information


D-lactate dehydratase / glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / cellular response to nutrient levels / : / protein folding chaperone / P-body / cytoplasmic stress granule / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGraille, M. / Leulliot, N. / Quevillon-Cheruel, S. / van Tilbeurgh, H.
CitationJournal: STRUCTURE / Year: 2004
Title: Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family
Authors: Graille, M. / Quevillon-Cheruel, S. / Leulliot, N. / Zhou, C.Z. / de la Sierra Gallay, I.L. / Jacquamet, L. / Ferrer, J.L. / Liger, D. / Poupon, A. / Janin, J. / van Tilbeurgh, H.
History
DepositionAug 29, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YDR533c protein
B: YDR533c protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8083
Polymers51,7162
Non-polymers921
Water7,422412
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.531, 166.196, 48.295
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein YDR533c protein


Mass: 25858.135 Da / Num. of mol.: 2 / Mutation: Ala22Met, Phe103Met, Ile143Met, Leu173Met
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YDR533c / Plasmid: pET9 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: Q04432
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.17 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 25-30% PEG 4000, 50mM Na/K phosphate buffer, 20mM DTT, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1drop
225-30 %PEG40001reservoir
350 mMsodium potassium phosphate1reservoirpH6.4
420 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002
RadiationMonochromator: Diamond(111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 38837 / Num. obs: 38837 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.081 / Net I/σ(I): 21.4
Reflection shellResolution: 1.9→1.96 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.44 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 185333 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 93.7 % / Rmerge(I) obs: 0.44

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of YDR533c solved by SAD method

Resolution: 1.9→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1874 -RANDOM
Rwork0.185 ---
all-38837 --
obs-37368 93.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.159 Å20 Å20 Å2
2---0.153 Å20 Å2
3----2.007 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 6 412 4038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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