+Open data
-Basic information
Entry | Database: PDB / ID: 3asv | ||||||
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Title | The Closed form of serine dehydrogenase complexed with NADP+ | ||||||
Components | Short-chain dehydrogenase/reductase SDR | ||||||
Keywords | OXIDOREDUCTASE / SDR family / Rossmann fold / short-chain dehydrogenase/reductase / L-allo-threonine dehydrogenase | ||||||
Function / homology | NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / PHOSPHATE ION Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||
Authors | Yamazawa, R. / Nakajima, Y. / Yoshimoto, T. / Ito, K. | ||||||
Citation | Journal: J.Biochem. / Year: 2011 Title: Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation. Authors: Yamazawa, R. / Nakajima, Y. / Mushiake, K. / Yoshimoto, T. / Ito, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3asv.cif.gz | 299.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3asv.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 3asv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/3asv ftp://data.pdbj.org/pub/pdb/validation_reports/as/3asv | HTTPS FTP |
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-Related structure data
Related structure data | 3asuSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 27277.887 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: XL1-Blue / Gene: EcDH1_2106, YdfG / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN (ESCHERICHI | |
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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: 2.26 Å3/Da / Density % sol: 45.54 % / Mosaicity: 0.906 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Na/K phosphate, lithium sulfate, Na acetate buffer, pH 4.5, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→50 Å / Num. obs: 39711 / % possible obs: 99.8 % / Redundancy: 4 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.126 / Χ2: 1.154 / Net I/σ(I): 6.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ASU Resolution: 2.7→20 Å / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 3235134 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: maximum likelihood target using amplitudes Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.1537 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.06 Å2 / Biso mean: 34.253 Å2 / Biso min: 10.32 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å / Total num. of bins used: 6
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Xplor file |
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