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Yorodumi- PDB-2c21: Specificity of the Trypanothione-dependednt Leishmania major Glyo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c21 | ||||||
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Title | Specificity of the Trypanothione-dependednt Leishmania major Glyoxalase I: Structure and biochemical comparison with the human enzyme | ||||||
Components | TRYPANOTHIONE-DEPENDENT GLYOXALASE I | ||||||
Keywords | LYASE / GLYOXALASE I / LEISHMANIA MAJOR / TRYPANOTHIONE / GLUTATHIONYLSPERMIDINE / METHYLGLYOXAL / DETOXIFICATION | ||||||
Function / homology | Function and homology information lactoylglutathione lyase / lactoylglutathione lyase activity / methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | LEISHMANIA MAJOR (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ariza, A. / Vickers, T.J. / Greig, N. / Armour, K.A. / Eggleston, I.M. / Fairlamb, A.H. / Bond, C.S. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2006 Title: Specificity of the Trypanothione-Dependent Leishmania Major Glyoxalase I: Structure and Biochemical Comparison with the Human Enzyme. Authors: Ariza, A. / Vickers, T.J. / Greig, N. / Armour, K.A. / Dixon, M.J. / Eggleston, I.M. / Fairlamb, A.H. / Bond, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c21.cif.gz | 202.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c21.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 2c21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c21_validation.pdf.gz | 457.3 KB | Display | wwPDB validaton report |
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Full document | 2c21_full_validation.pdf.gz | 461.6 KB | Display | |
Data in XML | 2c21_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 2c21_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c2/2c21 ftp://data.pdbj.org/pub/pdb/validation_reports/c2/2c21 | HTTPS FTP |
-Related structure data
Related structure data | 1fa8S 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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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 3 - 141 / Label seq-ID: 6 - 144
NCS oper:
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 16621.896 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) LEISHMANIA MAJOR (eukaryote) / Strain: FRIEDLIN A1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q68RJ8, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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-Non-polymers , 5 types, 855 molecules
#2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-MPD / ( #4: Chemical | #5: Chemical | #6: 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: 2.24 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | pH: 8 / Details: 62% (V/V) MPD, 100MM TRIS-HCL PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 16, 2004 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DIAMOND (111), GE (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2→60 Å / Num. obs: 67613 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 28.36 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 4.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FA8 Resolution: 2→129.1 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 6.709 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.143 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.53 Å2
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Refinement step | Cycle: LAST / Resolution: 2→129.1 Å
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Refine LS restraints |
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