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Yorodumi- PDB-2tod: ORNITHINE DECARBOXYLASE FROM TRYPANOSOMA BRUCEI K69A MUTANT IN CO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2tod | ||||||
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Title | ORNITHINE DECARBOXYLASE FROM TRYPANOSOMA BRUCEI K69A MUTANT IN COMPLEX WITH ALPHA-DIFLUOROMETHYLORNITHINE | ||||||
Components | PROTEIN (ORNITHINE DECARBOXYLASE) | ||||||
Keywords | LYASE / POLYAMINE METABOLISM / PYRIDOXAL 5'-PHOSPHATE / ALPHA-BETA BARREL | ||||||
Function / homology | Function and homology information ornithine decarboxylase / putrescine biosynthetic process from ornithine / ornithine decarboxylase activity / polyamine biosynthetic process Similarity search - Function | ||||||
Biological species | Trypanosoma brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Grishin, N.V. / Osterman, A.L. / Brooks, H.B. / Phillips, M.A. / Goldsmith, E.J. | ||||||
Citation | Journal: Biochemistry / Year: 1999 Title: X-ray structure of ornithine decarboxylase from Trypanosoma brucei: the native structure and the structure in complex with alpha-difluoromethylornithine. Authors: Grishin, N.V. / Osterman, A.L. / Brooks, H.B. / Phillips, M.A. / Goldsmith, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tod.cif.gz | 305.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tod.ent.gz | 243.7 KB | Display | PDB format |
PDBx/mmJSON format | 2tod.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/to/2tod ftp://data.pdbj.org/pub/pdb/validation_reports/to/2tod | HTTPS FTP |
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-Related structure data
Related structure data | 1qu4C 7odcS C: citing same article (ref.) 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 47004.359 Da / Num. of mol.: 4 / Mutation: K69A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): B21/DG3 / References: UniProt: P07805, ornithine decarboxylase #2: Chemical | ChemComp-DMO / #3: Chemical | ChemComp-PLP / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 32 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 16% PEG 3350, 0.2 M SOLIUM ACETATE, 100MM HEPES PH 7.5, 20MG/ML PROTEIN DILUTED TWICE, 16C, pH 7.0 | ||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / pH: 8 / Method: vapor diffusion, hanging dropDetails: Grishin, N.V., (1996) Proteins Struct. Funct. Genet., 24, 272. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.908 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 103282 / % possible obs: 97.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.9 |
Reflection | *PLUS Num. measured all: 339850 |
Reflection shell | *PLUS % possible obs: 61.7 % / Mean I/σ(I) obs: 1.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 7ODC Resolution: 2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2→8 Å
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Software | *PLUS Name: 'REFMAC, X-PLOR, CNS' / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 1 / % reflection Rfree: 10 % / Rfactor obs: 0.212 / Rfactor Rfree: 0.27 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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