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Yorodumi- PDB-2dab: L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dab | ||||||
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Title | L201A MUTANT OF D-AMINO ACID AMINOTRANSFERASE COMPLEXED WITH PYRIDOXAL-5'-PHOSPHATE | ||||||
Components | D-AMINO ACID AMINOTRANSFERASE | ||||||
Keywords | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / D-AMINO ACID / D-ALANINE / ALPHA-KETOGLUTAMIC ACID | ||||||
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 | Bacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sugio, S. / Kashima, A. / Kishimoto, K. / Peisach, D. / Petsko, G.A. / Ringe, D. / Yoshimura, T. / Esaki, N. | ||||||
Citation | Journal: Protein Eng. / Year: 1998 Title: Crystal structures of L201A mutant of D-amino acid aminotransferase at 2.0 A resolution: implication of the structural role of Leu201 in transamination. Authors: Sugio, S. / Kashima, A. / Kishimoto, K. / Peisach, D. / Petsko, G.A. / Ringe, D. / Yoshimura, T. / Esaki, N. #1: Journal: J.Biochem.(Tokyo) / Year: 1995 Title: Role of Leucine 201 of Thermostable D-Amino Acid Aminotransferase from a Thermophile, Bacillus Sp. Ym-1 Authors: Kishimoto, K. / Yoshimura, T. / Esaki, N. / Sugio, S. / Manning, J.M. / Soda, K. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dab.cif.gz | 121.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dab.ent.gz | 98.1 KB | Display | PDB format |
PDBx/mmJSON format | 2dab.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dab_validation.pdf.gz | 454 KB | Display | wwPDB validaton report |
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Full document | 2dab_full_validation.pdf.gz | 456.2 KB | Display | |
Data in XML | 2dab_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 2dab_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/2dab ftp://data.pdbj.org/pub/pdb/validation_reports/da/2dab | HTTPS FTP |
-Related structure data
Related structure data | 1a0gC 1daaS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.193696, 0.080777, 0.977731), Vector: |
-Components
#1: Protein | Mass: 32269.826 Da / Num. of mol.: 2 / Mutation: L201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: YM-1 / Plasmid: PAZZI / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P19938, D-amino-acid transaminase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.5 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 9 Details: THE PROTEIN WAS CRYSTALLIZED FROM 30% PEG3350, 500MM SODIUM ACETATE, 100MM TRIS/HCL, 5MM SODIUM AZIDE, PH9.0 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop solution was mixed with an equal volume of reservoir solution | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: May 27, 1996 / Details: YALE MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→91.63 Å / Num. obs: 48809 / % possible obs: 81 % / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.09 |
Reflection shell | Resolution: 1.79→1.9 Å / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 1.57 / % possible all: 48.3 |
Reflection shell | *PLUS % possible obs: 48.3 % / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1DAA Resolution: 2→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: A RESOLUTION-DEPENDENT WEIGHTING SCHEME WAS EMPLOYED, AND A BULK SOLVENT CORRECTION WAS APPLIED.
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Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.288 |