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- PDB-2ay3: AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-(3,4-DIMETHOXYPHENYL)... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ay3 | ||||||
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Title | AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-(3,4-DIMETHOXYPHENYL)PROPIONIC ACID | ||||||
![]() | AROMATIC AMINO ACID AMINOTRANSFERASE | ||||||
![]() | AMINOTRANSFERASE | ||||||
Function / homology | ![]() aromatic-amino-acid transaminase / L-phenylalanine:2-oxoglutarate aminotransferase activity / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / aspartate catabolic process / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Okamoto, A. / Hirotsu, K. / Kagamiyama, H. | ||||||
![]() | ![]() Title: The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity. Authors: Okamoto, A. / Ishii, S. / Hirotsu, K. / Kagamiyama, H. #1: ![]() Title: Crystal Structures of Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Substrate Recognition Site Constructed by Rearrangement of Hydrogen Bond Network Authors: Okamoto, A. / Nakai, Y. / Hayashi, H. / Hirotsu, K. / Kagamiyama, H. #2: ![]() Title: Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Model Enzyme for the Study of Dual Substrate Recognition Mechanism Authors: Oue, S. / Okamoto, A. / Nakai, Y. / Nakahira, M. / Shibatani, T. / Hayashi, H. / 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 | ![]() | 160.7 KB | Display | ![]() |
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PDB format | ![]() | 130.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.4 KB | Display | ![]() |
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Full document | ![]() | 421.9 KB | Display | |
Data in XML | ![]() | 18.1 KB | Display | |
Data in CIF | ![]() | 28.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ay1C ![]() 2ay2C ![]() 2ay4C ![]() 2ay5C ![]() 2ay6C ![]() 2ay7C ![]() 2ay8C ![]() 2ay9C ![]() 1ay8S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.956554, 0.096517, -0.275116), Vector: |
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Components
#1: Protein | Mass: 42779.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P95468, aromatic-amino-acid transaminase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANSFERASE ...THE RESIDUE NUMBERING IS BASED ON THE SEQUENCE OF PIG CYTOSOLIC ASPARTATE AMINOTRANS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.8 % | ||||||||||||||||||||||||
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Crystal grow | pH: 5.7 / Details: pH 5.7 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: micro-seeding | ||||||||||||||||||||||||
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 / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→86.8 Å / Num. obs: 26603 / % possible obs: 99.1 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 12.1 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 108 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 16 / % possible all: 97.9 |
Reflection | *PLUS Num. measured all: 81817 |
Reflection shell | *PLUS % possible obs: 97.9 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1AY8 Resolution: 2.4→6 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 25.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.54 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.208 |