[English] 日本語
Yorodumi- PDB-1b9i: CRYSTAL STRUCTURE OF 3-AMINO-5-HYDROXYBENZOIC ACID (AHBA) SYNTHASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b9i | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF 3-AMINO-5-HYDROXYBENZOIC ACID (AHBA) SYNTHASE | ||||||
Components | PROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE) | ||||||
Keywords | RIFAMYCIN BIOSYNTHESIS (RIFD GENE) | ||||||
Function / homology | Function and homology information 3-amino-5-hydroxybenzoate synthase / dTDP-4-amino-4,6-dideoxygalactose transaminase activity / Transferases; Transferring nitrogenous groups; Transaminases / polysaccharide biosynthetic process / antibiotic biosynthetic process / pyridoxal phosphate binding / lyase activity Similarity search - Function | ||||||
Biological species | Amycolatopsis mediterranei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Eads, J.C. / Beeby, M. / Scapin, G. / Yu, T.-W. / Floss, H.G. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase. Authors: Eads, J.C. / Beeby, M. / Scapin, G. / Yu, T.W. / Floss, H.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1b9i.cif.gz | 89.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1b9i.ent.gz | 68.2 KB | Display | PDB format |
PDBx/mmJSON format | 1b9i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b9i_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1b9i_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 1b9i_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 1b9i_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b9i ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b9i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 42248.598 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Plasmid: PRSETB(EAHBA6) / Production host: Escherichia coli (E. coli) / References: UniProt: O52552 |
---|---|
#2: Chemical | ChemComp-PXG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
---|
-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 60 % / Description: IN-HOUSE (CUKA) DATA MERGED WITH SRS DATA | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 133 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 / Wavelength: 1.4888 Å | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2→42.3 Å / Num. obs: 38950 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.1 | |||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 4 / % possible all: 89 | |||||||||
Reflection shell | *PLUS % possible obs: 89 % |
-Processing
Software | Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: XPLOR USED IN EARLIER STAGES OF REFINEMENT
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |