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Yorodumi- PDB-2w2k: Crystal structure of the apo forms of Rhodotorula graminis D- man... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w2k | ||||||
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Title | Crystal structure of the apo forms of Rhodotorula graminis D- mandelate dehydrogenase at 1.8A. | ||||||
Components | (D-MANDELATE DEHYDROGENASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / MANDELATE DEHYDROGENASE / 2-HYDROXYACID DEHYDROGENASE | ||||||
Function / homology | Function and homology information hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / cytosol Similarity search - Function | ||||||
Biological species | RHODOTORULA GRAMINIS (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Vachieri, S.G. / Cole, A.R. / Bagneris, C. / Baker, D.P. / Fewson, C.A. / Basak, A.K. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Apo and Holo Forms of Rhodotorula Graminis D(-)-Mandelate Dehydrogenase Authors: Vachieri, S.G. / Cole, A.R. / Bagneris, C. / Baker, D.P. / Fewson, C.A. / Basak, A.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w2k.cif.gz | 161 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w2k.ent.gz | 125.9 KB | Display | PDB format |
PDBx/mmJSON format | 2w2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2w2k_validation.pdf.gz | 425.3 KB | Display | wwPDB validaton report |
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Full document | 2w2k_full_validation.pdf.gz | 431.9 KB | Display | |
Data in XML | 2w2k_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 2w2k_validation.cif.gz | 51.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w2/2w2k ftp://data.pdbj.org/pub/pdb/validation_reports/w2/2w2k | HTTPS FTP |
-Related structure data
Related structure data | 2w2lC 1mx3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37997.266 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) RHODOTORULA GRAMINIS (fungus) / Strain: KGX39 / References: UniProt: Q7LLW9 |
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#2: Protein | Mass: 37983.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: C.A.FEWSON / Source: (natural) RHODOTORULA GRAMINIS (fungus) / Strain: KGX39 / References: UniProt: Q7LLW9 |
#3: Water | ChemComp-HOH / |
Sequence details | IMPORTANT SEQUENCE DISCREPANCIES EXIST WITH THE UNIPROT ENTRY. THE AUTHOR OF THE ENTRY HAS BEEN ...IMPORTANT SEQUENCE DISCREPANC |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50 % / Description: NONE |
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Crystal grow | pH: 6 Details: 100 MM MES-NAOH PH 6.0, 200 MM NACL, 20% PEG-MME5K, 1% DIOXANE, 1MM DTT. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.8 Å / Num. obs: 59834 / % possible obs: 95.1 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 0.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 9 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MX3 Resolution: 1.85→25.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.279 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PRO 2 A AND PRO 2 B WERE MODELLED AS ALA DUE TO DISORDERED SIDE CHAIN DENSITY MET 1 A, MET 1 B, SER 346 B WERE NOT MODELLED DUE TO DISORDERED DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.12 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→25.96 Å
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Refine LS restraints |
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