[English] 日本語
![](img/lk-miru.gif)
- PDB-1pvy: 3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pvy | ||||||
---|---|---|---|---|---|---|---|
Title | 3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii in complex with ribulose 5-phosphate | ||||||
![]() | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
![]() | ISOMERASE / riboflavin biosynthesis | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Steinbacher, S. / Schiffmann, S. / Richter, G. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
![]() | ![]() 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: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 110.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 463.3 KB | Display | |
Data in XML | ![]() | 23 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pvwSC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() Gene: MJ0055 / Plasmid: pNCO-MJ / Production host: ![]() ![]() References: UniProt: Q60364, Isomerases; Intramolecular transferases; Transferring other groups #2: Sugar | #3: Chemical | #4: Chemical | ChemComp-CA / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.27 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() |
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 |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1PVW Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|