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Yorodumi- PDB-1bw0: CRYSTAL STRUCTURE OF TYROSINE AMINOTRANSFERASE FROM TRYPANOSOMA CRUZI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bw0 | ||||||
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Title | CRYSTAL STRUCTURE OF TYROSINE AMINOTRANSFERASE FROM TRYPANOSOMA CRUZI | ||||||
Components | PROTEIN (TYROSINE AMINOTRANSFERASE) | ||||||
Keywords | TRANSFERASE / TYROSINE CATABOLISM / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / PLP | ||||||
Function / homology | Function and homology information tyrosine transaminase / tyrosine catabolic process / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine catabolic process / biosynthetic process / pyridoxal phosphate binding / mitochondrion Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Blankenfeldt, W. / Montemartini, M. / Hunter, G.R. / Kalisz, H.M. / Nowicki, C. / Hecht, H.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode. Authors: Blankenfeldt, W. / Nowicki, C. / Montemartini-Kalisz, M. / Kalisz, H.M. / Hecht, H.J. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and Preliminary X-Ray Analysis of Tyrosine Aminotransferase from Trypanosoma Cruzi Epimastigotes Authors: Nowicki, C. / Montemartini, M. / Hunter, G.R. / Blankenfeldt, W. / Hecht, H.J. #2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: Aromatic Amino Acid Transamination and Methionine Recycling in Trypanosomatids Authors: Berger, B.J. / Dai, W.W. / Wang, H. / Stark, R.E. / Cerami, A. #3: Journal: Fems Microbiol.Lett. / Year: 1994 Title: Production of Aromatic Alpha-Hydroxyacids by Epimastigotes of Trypanosoma Cruzi, and its Possible Role in Nadh Reoxidation Authors: Montemartini, M. / Santome, J.A. / Cazzulo, J.J. / Nowicki, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bw0.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bw0.ent.gz | 134.1 KB | Display | PDB format |
PDBx/mmJSON format | 1bw0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bw0_validation.pdf.gz | 437.8 KB | Display | wwPDB validaton report |
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Full document | 1bw0_full_validation.pdf.gz | 446 KB | Display | |
Data in XML | 1bw0_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 1bw0_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/1bw0 ftp://data.pdbj.org/pub/pdb/validation_reports/bw/1bw0 | HTTPS FTP |
-Related structure data
Related structure data | 1artS S: Starting model for refinement |
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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: (0.57939, 0.761052, 0.291731), Vector: |
-Components
#1: Protein | Mass: 46449.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE PROTEIN WAS PURIFIED FROM TRYPANOSOMA CRUZI EPIMASTIGOTES. Source: (natural) Trypanosoma cruzi (eukaryote) / Strain: TUL 0 / References: UniProt: P33447, tyrosine transaminase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 5 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||
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Crystal grow | pH: 7 Details: DIALYSIS OF 2.6 MG/ML PROTEIN AGAINST 25 % (W/W) PEG 8000, 5 MM PLP, 0.1 M PHOSPHATE/CITRATE, PH 7.0, 285 K | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 285 K / Method: microdialysis | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Source: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418 |
Detector | Type: SIEMENS X1000 / Detector: AREA DETECTOR / Date: Jun 15, 1996 / Details: COLLIMATOR |
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→10 Å / Num. obs: 24668 / % possible obs: 78.4 % / Redundancy: 1.7 % / Biso Wilson estimate: 30.17 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 6 / % possible all: 47 |
Reflection shell | *PLUS % possible obs: 47 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ART Resolution: 2.5→10 Å / SU B: 5.63 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.31
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Displacement parameters | Biso mean: 25.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.51 Å / Lowest resolution: 2.6 Å / Rfactor Rfree: 0.294 / Rfactor obs: 0.211 |