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Open data
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Basic information
Entry | Database: PDB / ID: 1qvz | ||||||
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Title | Crystal structure of the S. cerevisiae YDR533c protein | ||||||
![]() | YDR533c protein | ||||||
![]() | structural genomics / unknown function / alpha/beta hydrolase fold / catalytic triad / heat shock protein | ||||||
Function / homology | ![]() D-lactate dehydratase / glyoxalase III activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / cellular response to nutrient levels / chaperone-mediated protein folding / protein folding chaperone / P-body / cytoplasmic stress granule / cellular response to oxidative stress / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Graille, M. / Leulliot, N. / Quevillon-Cheruel, S. / van Tilbeurgh, H. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.4 KB | Display | ![]() |
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PDB format | ![]() | 87.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 440.6 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 34.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 25985.598 Da / Num. of mol.: 2 / Mutation: Ala22SeMet, Phe103SeMet, Ile143SeMe, Leu173SeMet Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: YDR533c / Plasmid: pET9 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.09 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→30 Å / Num. all: 95497 / Num. obs: 95497 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.8 Å2 / Rsym value: 0.04 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.73→1.83 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.18 / % possible all: 78.9 |
Reflection | *PLUS Num. measured all: 336312 / Rmerge(I) obs: 0.04 |
Reflection shell | *PLUS % possible obs: 78.9 % / Rmerge(I) obs: 0.18 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.1654 Å2 / ksol: 0.389519 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→19.65 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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