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- PDB-1czc: ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH GLUTARIC ACID -
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Open data
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Basic information
Entry | Database: PDB / ID: 1czc | ||||||
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Title | ASPARTATE AMINOTRANSFERASE MUTANT ATB17/139S/142N WITH GLUTARIC ACID | ||||||
![]() | PROTEIN (ASPARTATE AMINOTRANSFERASE) | ||||||
![]() | TRANSFERASE / ASPARTATE AMINOTRANSFERASE / SUBSTRATE SPECIFICITY | ||||||
Function / homology | ![]() L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic 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 | ![]() | 94.2 KB | Display | ![]() |
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PDB format | ![]() | 69.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1czeC ![]() 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-GUA / |
#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 GLUTARIC ACID, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||
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 15, 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: 2.5→75 Å / Num. obs: 16658 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.0536 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.5→2.8 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.088 / Mean I/σ(I) obs: 64 / % possible all: 97.5 |
Reflection | *PLUS Num. measured all: 61781 |
Reflection shell | *PLUS % possible obs: 97.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1YOO Resolution: 2.5→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: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.65 Å / Rfactor Rfree error: 0.018 / 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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