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- PDB-1cze: ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH SUCCINIC ACID -
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Open data
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Basic information
Entry | Database: PDB / ID: 1cze | ||||||
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Title | ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH SUCCINIC ACID | ||||||
![]() | ASPARTATE AMINOTRANSFERASE | ||||||
![]() | TRANSFERASE / ASPARTATE AMINOTRANSFERASE / SUBSTRATE SPECIFICITY | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Okamoto, A. / Oue, S. / Yano, T. / Kagamiyama, H. | ||||||
![]() | ![]() Title: Cocrystallization of a mutant aspartate aminotransferase with a C5-dicarboxylic substrate analog: structural comparison with the enzyme-C4-dicarboxylic analog complex. Authors: Oue, S. / Okamoto, A. / Yano, T. / Kagamiyama, H. #1: ![]() Title: Redesigning the Substrate Specificity of an Enzyme by Cumulative Effects of the Mutations of Non-Active Site Residues Authors: Oue, S. / Okamoto, A. / Yano, T. / Kagamiyama, H. #2: ![]() Title: Directed Evolution of an Aspartate Aminotransferase with New Substrate Specificities Authors: Yano, T. / Oue, S. / Kagamiyama, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.4 KB | Display | ![]() |
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PDB format | ![]() | 68.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 399.4 KB | Display | ![]() |
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Full document | ![]() | 404.8 KB | Display | |
Data in XML | ![]() | 9.9 KB | Display | |
Data in CIF | ![]() | 15 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1czcC ![]() 1yooS S: Starting model for refinement C: citing same article ( |
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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: 43662.207 Da / Num. of mol.: 1 Mutation: A11T,F24L,N34D,I37M,K41N,K126R,A269T,A293V, N297S,S311G,I353T,S361F,S363G, V387L,M397L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-SIN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.9 % | |||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.7M AMMONIUM SULFATE, 0.1 M SODIUM HEPES, 0.167 M SUCCINIC ACID, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃Details: 3 micro litter of protein was mixed with 1 microl litter of sodium succinate and 3 micro litter of a 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: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 16, 1999 / Details: MIRROR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→75 Å / Num. obs: 18949 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 3.8 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.0643 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3 % / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 42.5 / % possible all: 99.4 |
Reflection | *PLUS Num. measured all: 71147 |
Reflection shell | *PLUS % possible obs: 99.4 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YOO Resolution: 2.4→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 21.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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