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Yorodumi- PDB-1snn: 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1snn | ||||||
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Title | 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.55 Å | ||||||
Authors | Steinbacher, S. / Schiffmann, S. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2004 Title: Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate. Authors: Steinbacher, S. / Schiffmann, S. / Bacher, A. / Fischer, M. #1: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1snn.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1snn.ent.gz | 83.6 KB | Display | PDB format |
PDBx/mmJSON format | 1snn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1snn_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 1snn_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 1snn_validation.xml.gz | 22.2 KB | Display | |
Data in CIF | 1snn_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/1snn ftp://data.pdbj.org/pub/pdb/validation_reports/sn/1snn | HTTPS FTP |
-Related structure data
Related structure data | 1pvyS S: Starting model for refinement |
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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 biological unit is identical to the assymmetric dimer |
-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: 1.97 Å3/Da / Density % sol: 37.1 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.283, 1.2823 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 15, 1999 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.55→20 Å / Num. all: 53846 / Num. obs: 53846 / % possible obs: 0.883 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 17.5 | |||||||||
Reflection shell | Resolution: 1.55→1.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1PVY Resolution: 1.55→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: The purpose of the present study was to unumbiguously identify a metal ion as zinc. Therefore a data set including the anomlaous data was collected at the zinc absorption edge. The structure ...Details: The purpose of the present study was to unumbiguously identify a metal ion as zinc. Therefore a data set including the anomlaous data was collected at the zinc absorption edge. The structure is virtually identical to the entry 1PVY. Therefore, a simple refinement was sufficient to "solve" the structure. The strcuture was refined against the data set, not containing the anomalous data.
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.55→20 Å
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Refine LS restraints |
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