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Yorodumi- PDB-1toj: Hydrocinnamic acid-bound structure of SRHEPT mutant of E. coli as... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1toj | ||||||
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Title | Hydrocinnamic acid-bound structure of SRHEPT mutant of E. coli aspartate aminotransferase | ||||||
Components | Aspartate aminotransferase | ||||||
Keywords | TRANSFERASE / aspartate aminotransferase hexamutant / SRHEPT | ||||||
Function / homology | Function and homology information L-phenylalanine biosynthetic process / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / aspartate catabolic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Chow, M.A. / McElroy, K.E. / Corbett, K.D. / Berger, J.M. / Kirsch, J.F. | ||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Narrowing substrate specificity in a directly evolved enzyme: the A293D mutant of aspartate aminotransferase Authors: Chow, M.A. / McElroy, K.E. / Corbett, K.D. / Berger, J.M. / Kirsch, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1toj.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1toj.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 1toj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1toj_validation.pdf.gz | 442.4 KB | Display | wwPDB validaton report |
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Full document | 1toj_full_validation.pdf.gz | 446.6 KB | Display | |
Data in XML | 1toj_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 1toj_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/1toj ftp://data.pdbj.org/pub/pdb/validation_reports/to/1toj | HTTPS FTP |
-Related structure data
Related structure data | 1toeC 1togC 1toiC 1tokC 1ahxS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a dimer, the second part of which is generated by the two-fold axis: -x+1, -z+1/2 |
-Components
#1: Protein | Mass: 43825.281 Da / Num. of mol.: 1 / Mutation: A12T,P13T,N34D,T109S,G261A,S285G,N297S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ASPC, B0928 / Plasmid: pJO2 / Production host: Escherichia coli (E. coli) / Strain (production host): MG204 / References: UniProt: P00509, aspartate transaminase |
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#2: Chemical | ChemComp-HCI / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 59 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: potassium phosphate, PLP, EDTA, DTT, PEG 400, N-methylmorpholine, ammonium sulfate, hydrocinnamic acid, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 23, 2003 |
Radiation | Monochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 40208 / Num. obs: 40208 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.04 / Net I/σ(I): 25 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3874 / Rsym value: 0.236 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AHX Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.6 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.916 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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