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Yorodumi- PDB-1arg: Aspartate aminotransferase, phospho-5'-pyridoxyl aspartate complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1arg | ||||||
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Title | Aspartate aminotransferase, phospho-5'-pyridoxyl aspartate complex | ||||||
Components | ASPARTATE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE (AMINOTRANSFERASE) | ||||||
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 / Resolution: 2.2 Å | ||||||
Authors | Malashkevich, V.N. / Jansonius, J.N. | ||||||
Citation | Journal: Eur.J.Biochem. / Year: 1995 Title: Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme. Authors: Graber, R. / Kasper, P. / Malashkevich, V.N. / Sandmeier, E. / Berger, P. / Gehring, H. / Jansonius, J.N. / Christen, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1arg.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1arg.ent.gz | 137.6 KB | Display | PDB format |
PDBx/mmJSON format | 1arg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1arg_validation.pdf.gz | 506.7 KB | Display | wwPDB validaton report |
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Full document | 1arg_full_validation.pdf.gz | 545.1 KB | Display | |
Data in XML | 1arg_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 1arg_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ar/1arg ftp://data.pdbj.org/pub/pdb/validation_reports/ar/1arg | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: CIS PROLINE - PRO A 138 / 2: CIS PROLINE - PRO A 195 / 3: CIS PROLINE - PRO B 138 / 4: CIS PROLINE - PRO B 195 | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, -0.00069, -0.00206), Vector: Details | MTRIX THE TRANSFORMATIONS PRESENTED ON MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG THE VARIOUS DOMAINS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. APPLIED TO TRANSFORMED TO MTRIX RESIDUES RESIDUES RMSD M1 A 5 .. A 409 B 5 .. B 409 0.196 | |
-Components
#1: Protein | Mass: 43619.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TY103 / Plasmid: PKDHE19 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.03 Å3/Da / Density % sol: 59.4 % |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
Crystal | *PLUS Density % sol: 57.9 % |
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 21, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Redundancy: 3.3 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.057 |
Reflection | *PLUS Highest resolution: 2.2 Å / Lowest resolution: 40 Å / Num. obs: 44764 / % possible obs: 93 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.057 |
-Processing
Software |
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Refinement | Resolution: 2.2→8 Å / Isotropic thermal model: B-CORRELATION METHOD / σ(F): 1 / Stereochemistry target values: ENGH AND HUBER /
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Solvent computation | Solvent model: MOEWS AND KRETSINGER, JMB (1975) 91,201-22 / Bsol: 253.9 Å2 / ksol: 0.725 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 26.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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