+Open data
-Basic information
Entry | Database: PDB / ID: 2vpm | ||||||
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Title | Trypanothione synthetase | ||||||
Components | TRYPANOTHIONE SYNTHETASE | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information trypanothione synthase / trypanothione synthase activity / ligase activity / cytoplasm Similarity search - Function | ||||||
Biological species | LEISHMANIA MAJOR (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Fyfe, P.K. / Oza, S.L. / Fairlamb, A.H. / Hunter, W.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Leishmania Trypanothione Synthetase-Amidase Structure Reveals a Basis for Regulation of Conflicting Synthetic and Hydrolytic Activities. Authors: Fyfe, P.K. / Oza, S.L. / Fairlamb, A.H. / Hunter, W.N. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vpm.cif.gz | 248.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vpm.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 2vpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vp/2vpm ftp://data.pdbj.org/pub/pdb/validation_reports/vp/2vpm | HTTPS FTP |
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-Related structure data
Related structure data | 2vobSC 2vpsC 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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-Components
#1: Protein | Mass: 74668.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN / Plasmid: PET15B-TEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q711P7, trypanothione synthase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-BR / | #4: Water | ChemComp-HOH / | Sequence details | HIS0 IN CHAINS A AND B CARRIED OVER FROM HIS-TAG AND PROTEASE CLEAVAGE SITE | |
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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: 3.35 Å3/Da / Density % sol: 64 % Description: MOLECULAR REPLACEMENT PERFORMED USING MONOMER A PDB ENTRY 2VOB |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9199 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 20, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9199 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→20 Å / Num. obs: 48090 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2VOB Resolution: 2.8→84.82 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.885 / SU B: 25.134 / SU ML: 0.253 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.723 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.83 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→84.82 Å
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Refine LS restraints |
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