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Yorodumi- PDB-1b9h: CRYSTAL STRUCTURE OF 3-AMINO-5-HYDROXYBENZOIC ACID (AHBA) SYNTHASE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b9h | ||||||
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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 / MIR / 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b9h.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b9h.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 1b9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b9h_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 1b9h_full_validation.pdf.gz | 452.5 KB | Display | |
Data in XML | 1b9h_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 1b9h_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/1b9h ftp://data.pdbj.org/pub/pdb/validation_reports/b9/1b9h | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42262.625 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 |
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#2: Chemical | ChemComp-PLP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 60 % Description: MAD DATA USED AS MIR EXPERIMENT, STATISTICS LISTED ARE FOR BEST MAD DATASET (IE NOT NATIVE) | ||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 133 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.5418,1.008,0.832 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→99 Å / Num. obs: 65659 / % possible obs: 99.6 % / Redundancy: 1.9 % / Rsym value: 3.8 / Net I/σ(I): 18.6 | ||||||||||||
Reflection shell | Resolution: 1.7→1.76 Å / Rsym value: 16.6 / % possible all: 100 | ||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.037 | ||||||||||||
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 2.6 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0 Details: XPLOR USED IN EARLIER STAGES OF REFINEMENT. RESIDUE 1 (MET) IS NOT PRESENT IN THE PROTEIN. RESIDUES 2-4 ARE NOT MODELED IN THE STRUCTURE (POOR ELECTRON DENSITY)
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |