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Yorodumi- PDB-1vl8: Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vl8 | ||||||
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Title | Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 A resolution | ||||||
Components | Gluconate 5-dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / TM0441 / GLUCONATE 5-DEHYDROGENASE / STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Gluconate 5-dehydrogenase (TM0441) from Thermotoga maritima at 2.07 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 | 1vl8.cif.gz | 120.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vl8.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vl8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/1vl8 ftp://data.pdbj.org/pub/pdb/validation_reports/vl/1vl8 | HTTPS FTP |
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-Related structure data
Related structure data | 1g6kS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 2 / Auth seq-ID: 5 - 255 / Label seq-ID: 17 - 267
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-Components
#1: Protein | Mass: 29410.531 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYS2, gluconate 5-dehydrogenase #2: Chemical | ChemComp-PO4 / | #3: Chemical | #4: Chemical | ChemComp-MG / | #5: 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: 3.89 Å3/Da / Density % sol: 68.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2 Details: Acetate pH 4.2, 35% Glycerol, 0.4M NH4H2PO3 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979127 |
Detector | Type: APS / Detector: CCD / Date: Feb 20, 2004 Details: water cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979127 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 61222 / % possible obs: 89.42 % / Redundancy: 6.89 % / Biso Wilson estimate: 32.51 Å2 / Rsym value: 0.088 / Net I/σ(I): 16.01 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 2.35 % / Mean I/σ(I) obs: 1.06 / Num. unique all: 4917 / Rsym value: 0.672 / % possible all: 72.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1g6k Resolution: 2.07→43.67 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.347 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.114 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.843 Å2
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Refinement step | Cycle: LAST / Resolution: 2.07→43.67 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 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.07→2.124 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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