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Yorodumi- PDB-1g2w: E177S MUTANT OF THE PYRIDOXAL-5'-PHOSPHATE ENZYME D-AMINO ACID AM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1g2w | ||||||
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Title | E177S MUTANT OF THE PYRIDOXAL-5'-PHOSPHATE ENZYME D-AMINO ACID AMINOTRANSFERASE | ||||||
Components | D-ALANINE AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / mutant / pyridoxal-5'-phosphate / water molecule / internal aldimine / aminotransferase / bacterial cell wall biosynthesis | ||||||
Function / homology | Function and homology information D-amino acid biosynthetic process / D-alanine-2-oxoglutarate aminotransferase activity / D-amino-acid transaminase / D-amino acid catabolic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Lepore, B.W. / Ringe, D. | ||||||
Citation | Journal: Biochemistry and Molecular Biology of Vitamin B6 and PQQ-dependent Proteins, 10th Annual International Symposium on Vitamin B6 Year: 2000 Title: Studies on an Active Site Residue, E177, That Affects Binding of the Coenzyme in D-Amino Acid Transaminase, and Mechanistic Studies on a Suicide Substrate Authors: van Ophem, P.W. / Lepore, B.W. / Kishimoto, K. / Ringe, D. / Manning, J.M. #1: Journal: Biochemistry / Year: 1995 Title: Crystal Structure of a D-amino Acid Aminotransferase: How the Protein Controls Stereoselectivity Authors: Sugio, S. / Petsko, G.A. / Manning, J.M. / Soda, K. / Ringe, D. #2: Journal: Biochemistry / Year: 1999 Title: Effects of the E177K mutation in D-amino acid aminotransaminase. Studies on an essential coenzyme anchoring group that contributes to stereochemical fidelity Authors: van Ophem, P.W. / Peisach, D. / Erickson, S.D. / Soda, K. / Ringe, D. / Manning, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1g2w.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1g2w.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1g2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1g2w_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 1g2w_full_validation.pdf.gz | 462.7 KB | Display | |
Data in XML | 1g2w_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 1g2w_validation.cif.gz | 32.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/1g2w ftp://data.pdbj.org/pub/pdb/validation_reports/g2/1g2w | HTTPS FTP |
-Related structure data
Related structure data | |
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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
#1: Protein | Mass: 32269.873 Da / Num. of mol.: 2 / Mutation: E177S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Plasmid: PICT113 / Production host: Escherichia coli (E. coli) References: UniProt: P83771, UniProt: P19938*PLUS, D-amino-acid transaminase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.4 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: resevoir: Tris-HCl, pH 8.5, 22-26% PEG 4K, 0.2-0.4M NaOAc, 1mM alpha-ketoglutarate, enzyme buffer: 50mM KPO4, pH 7.2, 200mM KCl, 1mM DTT, 10uM PLP , VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 29, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27 Å / Num. all: 303396 / Num. obs: 96070 / % possible obs: 86 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 27.3 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.05→2.14 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.34 / Num. unique all: 1974 / % possible all: 92 |
Reflection | *PLUS % possible obs: 85.4 % / Num. measured all: 303396 |
Reflection shell | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 1.86 Å / % possible obs: 97.5 % / Rmerge(I) obs: 0.244 |
-Processing
Software |
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Refinement | Resolution: 2→6 Å / Cross valid method: CNS free-R value test / σ(F): 1 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target function on amplitudes
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Solvent computation | Solvent model: CNS bulk solvent model | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.12 Å / Total num. of bins used: 6
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 27 Å / σ(F): 1 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2 Å / Rfactor Rwork: 0.249 |