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Yorodumi- PDB-3wnv: Crystal structure of a glyoxylate reductase from Paecilomyes ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wnv | ||||||
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Title | Crystal structure of a glyoxylate reductase from Paecilomyes thermophila | ||||||
Components | glyoxylate reductase | ||||||
Keywords | OXIDOREDUCTASE / Glyoxylate reductase / Paecilomyes thermophila / three-dimensional structure / cofactor specificity | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding Similarity search - Function | ||||||
Biological species | Paecilomyces sp. J18 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Duan, X. / Hu, S. / Zhou, P. / Zhou, Y. / Jiang, Z. | ||||||
Citation | Journal: Enzyme.Microb.Technol. / Year: 2014 Title: Characterization and crystal structure of a first fungal glyoxylate reductase from Paecilomyes thermophila Authors: Duan, X. / Hu, S. / Zhou, P. / Zhou, Y. / Liu, Y. / Jiang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wnv.cif.gz | 279.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wnv.ent.gz | 226.6 KB | Display | PDB format |
PDBx/mmJSON format | 3wnv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wnv_validation.pdf.gz | 441.2 KB | Display | wwPDB validaton report |
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Full document | 3wnv_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 3wnv_validation.xml.gz | 30.3 KB | Display | |
Data in CIF | 3wnv_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/3wnv ftp://data.pdbj.org/pub/pdb/validation_reports/wn/3wnv | HTTPS FTP |
-Related structure data
Related structure data | 2w2lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35953.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paecilomyces sp. J18 (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0B4J185*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES buffer pH 6.5, 0.01M cobalt (II) chloride, 1.8M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2012 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 83856 / Num. obs: 82515 / % possible obs: 98.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 18.81 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 13.95 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.79 / Num. unique all: 3992 / Rsym value: 0.51 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2w2l Resolution: 1.75→49.398 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 23.35 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→49.398 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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Refinement TLS params. | Method: refined / Origin x: 7.6227 Å / Origin y: 9.9584 Å / Origin z: 37.6012 Å
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Refinement TLS group | Selection details: all |