[English] 日本語
Yorodumi- PDB-4ao9: Biochemical properties and crystal structure of a novel beta- phe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ao9 | ||||||
---|---|---|---|---|---|---|---|
Title | Biochemical properties and crystal structure of a novel beta- phenylalanine aminotransferase from Variovorax paradoxus | ||||||
Components | BETA-PHENYLALANINE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | VARIOVORAX PARADOXUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Crismaru, C.G. / Wybenga, G.G. / Szymanski, W. / Wijma, H.J. / Wu, B. / deWildeman, S. / Poelarends, G.J. / Dijkstra, B.W. / Janssen, D.B. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2013 Title: Biochemical Properties and Crystal Structure of a Novel Beta-Phenylalanine Aminotransferase from Variovorax Paradoxus Authors: Crismaru, C.G. / Wybenga, G.G. / Szymanski, W. / Wijma, H.J. / Wu, B. / Dewildeman, S. / Poelarends, G.J. / Dijkstra, B.W. / Janssen, D.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4ao9.cif.gz | 326.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4ao9.ent.gz | 265.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ao9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ao9_validation.pdf.gz | 454.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4ao9_full_validation.pdf.gz | 456.1 KB | Display | |
Data in XML | 4ao9_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 4ao9_validation.cif.gz | 53.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/4ao9 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/4ao9 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.8866, -0.2899, 0.3603), Vector: |
-Components
#1: Protein | Mass: 48634.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SCHIFF BASE BETWEEN K267 AND THE C4A ATOM OF THE PLP COFACTOR Source: (gene. exp.) VARIOVORAX PARADOXUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: H8WR05*PLUS #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE HAS BEEN SUBMITTED TO THE UNIPROTKB DATABASE, VALIDATION | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.6 % / Description: NONE |
---|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.42 Å / Num. obs: 148964 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: MES_BFAT_HOLO Resolution: 1.5→46.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.983 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.063 / 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 WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.386 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.42 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|