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Yorodumi- PDB-1v93: 5,10-Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1v93 | ||||||
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Title | 5,10-Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8 | ||||||
Components | 5,10-Methylenetetrahydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / 5 / 10-methylenetetrahydrofolate reductase / methylenetetrahydrofolate reductase / flavoprotein / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information methylenetetrahydrofolate reductase [NAD(P)H] / methylenetetrahydrofolate reductase (NADPH) activity / methylenetetrahydrofolate reductase (NADH) activity / methionine metabolic process / tetrahydrofolate interconversion / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Nakajima, Y. / Miyahara, I. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of 5,10-Methylenetetrahydrofolate reductase from Thermus thermophilus HB8 Authors: Nakajima, Y. / Miyahara, I. / Hirotsu, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1v93.cif.gz | 78.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1v93.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 1v93.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1v93_validation.pdf.gz | 472.1 KB | Display | wwPDB validaton report |
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Full document | 1v93_full_validation.pdf.gz | 475.4 KB | Display | |
Data in XML | 1v93_validation.xml.gz | 7.6 KB | Display | |
Data in CIF | 1v93_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/1v93 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/1v93 | HTTPS FTP |
-Related structure data
Related structure data | 1b5tS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33050.887 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RA47, EC: 1.7.99.5 | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | ChemComp-DIO / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.72 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 26-30% Dioxane, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 27, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 67109 / Num. obs: 24438 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.14 / Net I/σ(I): 2.8 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 2.2 / Num. unique all: 3482 / Rsym value: 0.281 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B5T Resolution: 1.9→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 26.9 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.97 Å
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