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Yorodumi- PDB-1njj: Crystal structure determination of T. brucei ornithine decarboxyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1njj | ||||||
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Title | Crystal structure determination of T. brucei ornithine decarboxylase bound to D-ornithine and to G418 | ||||||
Components | ornithine decarboxylase | ||||||
Keywords | LYASE / ornithine decarboxylase / ODC / PLP / pyridoxal 5'-phosphate / D-ornithine / G418 | ||||||
Function / homology | Function and homology information ornithine decarboxylase / ornithine decarboxylase activity / polyamine biosynthetic process Similarity search - Function | ||||||
Biological species | Trypanosoma brucei gambiense (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Jackson, L.K. / Goldsmith, E.J. / Phillips, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: X-ray Structure Determination of Trypanosoma brucei Ornithine Decarboxylase Bound to D-Ornithine and to G418: INSIGHTS INTO SUBSTRATE BINDING AND ODC CONFORMATIONAL FLEXIBILITY. Authors: Jackson, L.K. / Goldsmith, E.J. / Phillips, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1njj.cif.gz | 290.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1njj.ent.gz | 234.8 KB | Display | PDB format |
PDBx/mmJSON format | 1njj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/1njj ftp://data.pdbj.org/pub/pdb/validation_reports/nj/1njj | HTTPS FTP |
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-Related structure data
Related structure data | 1f3tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47150.590 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei gambiense (eukaryote) Species: Trypanosoma brucei / Strain: gambiense / Plasmid: PODC29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9TZZ6, ornithine decarboxylase #2: Chemical | #3: Chemical | ChemComp-ORX / #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: 2.82 Å3/Da / Density % sol: 56.11 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Peg 3350, Hepes, DTT, NaCl, D-ornithine, G418, butyrolactone, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 16K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 98.5 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 63372 / % possible obs: 96.7 % / Redundancy: 4 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / % possible all: 93.9 |
Reflection | *PLUS Num. measured all: 253681 |
Reflection shell | *PLUS % possible obs: 93.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1f3t with waters, K69, C360 and putrescine removed Resolution: 2.45→35 Å / σ(F): 2 / σ(I): 2
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Displacement parameters | Biso mean: 45.1 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→35 Å
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LS refinement shell | Resolution: 2.45→2.54 Å
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Refinement | *PLUS Rfactor Rwork: 0.26 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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