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Yorodumi- PDB-1vp5: Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vp5 | ||||||
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Title | Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution | ||||||
Components | 2,5-diketo-D-gluconic acid reductase | ||||||
Keywords | OXIDOREDUCTASE / TM1009 / 2 / 5-diketo-d-gluconic acid reductase (ec 1.1.1.274) / structural genomics / Joint Center for Structural Genomics / JCSG / PSI / Protein Structure Initiative | ||||||
Function / homology | Function and homology information D-threo-aldose 1-dehydrogenase activity / aldose reductase (NADPH) activity / nucleotide binding / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of 2,5-diketo-D-gluconic acid reductase (TM1009) from Thermotoga maritima at 2.40 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vp5.cif.gz | 132.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vp5.ent.gz | 104.2 KB | Display | PDB format |
PDBx/mmJSON format | 1vp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vp5_validation.pdf.gz | 963.7 KB | Display | wwPDB validaton report |
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Full document | 1vp5_full_validation.pdf.gz | 970.3 KB | Display | |
Data in XML | 1vp5_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 1vp5_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/1vp5 ftp://data.pdbj.org/pub/pdb/validation_reports/vp/1vp5 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 1 / Auth seq-ID: 2 - 284 / Label seq-ID: 14 - 296
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-Components
#1: Protein | Mass: 34749.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1009 / Production host: Escherichia coli (E. coli) References: UniProt: Q9X0A2, 2,5-didehydrogluconate reductase (2-dehydro-D-gluconate-forming) #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.73 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6 Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.000034 |
Detector | Type: ADSC / Detector: CCD / Date: Apr 3, 2004 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000034 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→24.93 Å / Num. obs: 28944 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 49.56 Å2 / Rsym value: 0.123 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 2124 / Rsym value: 0.83 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: REFINEMENT STARTING MODEL Resolution: 2.4→24.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.357 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.294 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.279 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→24.93 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4367 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.4→2.462 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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