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

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Basic information

Entry
Database: PDB / ID: 1qvv
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: 2.35 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: Version format compliance
Revision 1.3Jul 15, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list ...pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YDR533c protein
B: YDR533c protein
C: YDR533c protein
D: YDR533c protein


Theoretical massNumber of molelcules
Total (without water)103,1124
Polymers103,1124
Non-polymers00
Water5,855325
1
A: YDR533c protein

D: YDR533c protein


Theoretical massNumber of molelcules
Total (without water)51,5562
Polymers51,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
2
B: YDR533c protein

C: YDR533c protein


Theoretical massNumber of molelcules
Total (without water)51,5562
Polymers51,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x+1/2,-y+3/2,-z+11
Unit cell
Length a, b, c (Å)67.019, 93.636, 151.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
YDR533c protein


Mass: 25777.922 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.25 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 26% PEG 4000, 50mM Na/K phosphate buffer, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19 mg/mlprotein1drop
226 %PEG40001reservoir
350 mMsodium potassium phosphate1reservoirpH6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.004 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 29, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 41388 / Num. obs: 41388 / % possible obs: 84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 29.3 Å2 / Rsym value: 0.083 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 1.75 / Rsym value: 0.498 / % possible all: 71.4
Reflection
*PLUS
Redundancy: 14.5 % / Num. measured all: 598140 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 71.4 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→29.47 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 379163 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1557 5 %RANDOM
Rwork0.228 ---
obs0.228 31354 77.3 %-
all-41388 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.1282 Å2 / ksol: 0.35398 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.23 Å20 Å20 Å2
2--4.71 Å20 Å2
3----8.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.35→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7227 0 0 325 7552
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 228 5.5 %
Rwork0.308 3920 -
obs--62.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79

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