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Yorodumi- PDB-2q7w: Structural Studies Reveals the Inactivation of E. coli L-aspartat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q7w | ||||||
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Title | Structural Studies Reveals the Inactivation of E. coli L-aspartate aminotransferase (S)-4,5-amino-dihydro-2-thiophenecarboxylic acid (SADTA) via two mechanisms at pH 6.0 | ||||||
Components | Aspartate aminotransferase | ||||||
Keywords | TRANSFERASE / mechanism-based inhibitor / PLP / SADTA / pH dependence | ||||||
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: 1.4 Å | ||||||
Authors | Liu, D. / Pozharski, E. / Lepore, B. / Fu, M. / Silverman, R.B. / Petsko, G.A. / Ringe, D. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Inactivation of Escherichia coli l-Aspartate Aminotransferase by (S)-4-Amino-4,5-dihydro-2-thiophenecarboxylic Acid Reveals "A Tale of Two Mechanisms". Authors: Liu, D. / Pozharski, E. / Lepore, B.W. / Fu, M. / Silverman, R.B. / Petsko, G.A. / Ringe, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q7w.cif.gz | 199.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q7w.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 2q7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q7w_validation.pdf.gz | 872.4 KB | Display | wwPDB validaton report |
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Full document | 2q7w_full_validation.pdf.gz | 886.3 KB | Display | |
Data in XML | 2q7w_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 2q7w_validation.cif.gz | 36.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/2q7w ftp://data.pdbj.org/pub/pdb/validation_reports/q7/2q7w | HTTPS FTP |
-Related structure data
Related structure data | 2qa3C 2qb2C 2qb3C 2qbtC 1amqS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The second part of the biological assembly is generated by the 2 fold axis: x, -y, -z |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43744.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aspC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P00509, aspartate transaminase |
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-Non-polymers , 5 types, 442 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-PSZ / | ||
#4: Chemical | ChemComp-PMP / | ||
#5: Chemical | ChemComp-GOL / #6: 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: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 6 Details: 25 mM potassium phosphate, 43% saturated ammonium sulfate, 20 mM SADTA, pH 6.0, EVAPORATION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2005 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→77 Å / Num. obs: 93239 / % possible obs: 97 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.7 / Num. unique all: 10020 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AMQ Resolution: 1.4→76.92 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.664 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.056 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.351 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→76.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.435 Å / Total num. of bins used: 20
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