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- PDB-2z9u: Crystal structure of pyridoxamine-pyruvate aminotransferase from ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2z9u | ||||||
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Title | Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti at 2.0 A resolution | ||||||
![]() | Aspartate aminotransferase | ||||||
![]() | TRANSFERASE / AMINOTRANSFERASE / PYRIDOXAMINE / PYRUVATE | ||||||
Function / homology | ![]() pyridoxamine-pyruvate transaminase / pyridoxamine-pyruvate transaminase activity / transaminase activity / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yoshikane, Y. / Yokochi, N. / Yamasaki, M. / Mizutani, K. / Ohnishi, K. / Mikami, B. / Hayashi, H. / Yagi, T. | ||||||
![]() | ![]() Title: Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099 Authors: Yoshikane, Y. / Yokochi, N. / Yamasaki, M. / Mizutani, K. / Ohnishi, K. / Mikami, B. / Hayashi, H. / Yagi, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.9 KB | Display | ![]() |
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PDB format | ![]() | 132.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.1 KB | Display | ![]() |
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Full document | ![]() | 455.6 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2z9vC ![]() 2z9wC ![]() 2z9xC ![]() 1vjoS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 41503.512 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q988B8, pyridoxamine-pyruvate transaminase #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.05 Details: 0.1M HEPES, 2M Ammonium sulfate, pH 8.05, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 10, 2006 |
Radiation | Monochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 58804 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.379 / Num. unique all: 5701 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ID 1VJO Resolution: 2→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.669 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.156 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.596 Å2
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Refinement step | Cycle: LAST / Resolution: 2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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