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Yorodumi- PDB-1pvy: 3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvy | ||||||
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Title | 3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | ISOMERASE / riboflavin biosynthesis | ||||||
Function / homology | Function and homology information 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Steinbacher, S. / Schiffmann, S. / Richter, G. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structure of 3,4-Dihydroxy-2-butanone 4-Phosphate Synthase from Methanococcus jannaschii in Complex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: IMPLICATIONS FOR THE CATALYTIC MECHANISM Authors: Steinbacher, S. / Schiffmann, S. / Richter, G. / Huber, R. / Bacher, A. / Fischer, M. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Biosynthesis of Riboflavin in Archaea Studies on the Mechanism of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase of Methanococcus jannaschii Authors: Fischer, M. / Romisch, W. / Schiffmann, S. / Kelly, M. / Oschkinat, H. / Steinbacher, S. / Huber, R. / Eisenreich, W. / Richter, G. / Bacher, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvy.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvy.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 1pvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pvy_validation.pdf.gz | 455 KB | Display | wwPDB validaton report |
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Full document | 1pvy_full_validation.pdf.gz | 463.3 KB | Display | |
Data in XML | 1pvy_validation.xml.gz | 23 KB | Display | |
Data in CIF | 1pvy_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvy ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvy | HTTPS FTP |
-Related structure data
Related structure data | 1pvwSC 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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1 |
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Unit cell |
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Details | the molecule is a dimer which is present in the asymmetric unit |
-Components
#1: Protein | Mass: 25781.553 Da / Num. of mol.: 2 / Mutation: H147S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0055 / Plasmid: pNCO-MJ / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 References: UniProt: Q60364, Isomerases; Intramolecular transferases; Transferring other groups #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-CA / #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: 1.95 Å3/Da / Density % sol: 36.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal grow | *PLUS Method: unknown / Details: Fischer, M., (2002) J. Biol. Chem., 277, 41410. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2001 / Details: Osmic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 42575 / Num. obs: 42575 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.4 / % possible all: 97.8 |
Reflection | *PLUS Rmerge(I) obs: 0.06 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PVW Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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