[English] 日本語
![](img/lk-miru.gif)
- PDB-1ofo: Crystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Hep... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1ofo | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Tyrosine Regulated 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae in Complex with 2-Phosphoglycolate | |||||||||
![]() | PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE | |||||||||
![]() | LYASE / BETA-ALPHA-BARREL / AROMATIC AMINO-ACID BIOSYNTHESIS SYNTHASE / ALDOLASE / SYNTHETASE / MANGANESE | |||||||||
Function / homology | ![]() 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / Schneider, T.R. | |||||||||
![]() | ![]() Title: Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism. Authors: Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / Schneider, T.R. #1: ![]() Title: Evolution of Feedback-Inhibited Beta /Alpha Barrel Isoenzymes by Gene Duplication and a Single Mutation Authors: Hartmann, M. / Schneider, T. / Pfeil, A. / Heinrich, G. / Lipscomb, W. / Braus, G. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 145.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 115.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.2 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 460.9 KB | Display | |
Data in XML | ![]() | 30 KB | Display | |
Data in CIF | ![]() | 43.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1oabC ![]() 1of8C ![]() 1ofaC ![]() 1ofbC ![]() 1ofpC ![]() 1ofqC ![]() 1ofrC ![]() 1hfbS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 39797.055 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: 2-PHOSPHOGLYCOLATE Source: (gene. exp.) ![]() ![]() Strain: RH1326 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.24 % |
---|---|
Crystal grow | pH: 8 / Details: pH 8.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→17.3 Å / Num. obs: 198507 / % possible obs: 95.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.0444 / Net I/σ(I): 19.77 |
Reflection shell | Resolution: 1.86→1.95 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.3035 / Mean I/σ(I) obs: 4.36 / % possible all: 89.1 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1HFB (MOLECULE A) Resolution: 1.86→17.3 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.62 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→17.3 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|