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Yorodumi- PDB-2v6u: High resolution crystal structure of pterin-4a-carbinolamine dehy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v6u | ||||||
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Title | High resolution crystal structure of pterin-4a-carbinolamine dehydratase from Toxoplasma gondii | ||||||
Components | PTERIN-4A-CARBINOLAMINE DEHYDRATASE | ||||||
Keywords | LYASE / PTERIN / ENZYME / TOXOPLASMA / DEHYDRATASE | ||||||
Function / homology | Function and homology information 4a-hydroxytetrahydrobiopterin dehydratase / 4-alpha-hydroxytetrahydrobiopterin dehydratase activity / tetrahydrobiopterin biosynthetic process / plastid Similarity search - Function | ||||||
Biological species | TOXOPLASMA GONDII (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Cameron, S. / Goldie, S.P. / Hunter, W.N. | ||||||
Citation | Journal: Mol.Biochem.Parasitol. / Year: 2008 Title: Crystal Structures of Toxoplasma Gondii Pterin-4A-Carbinolamine Dehydratase and Comparisons with Mammalian and Parasite Orthologues. Authors: Cameron, S. / Fyffe, S.A. / Goldie, S.P. / Hunter, W.N. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v6u.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v6u.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 2v6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v6u_validation.pdf.gz | 428.6 KB | Display | wwPDB validaton report |
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Full document | 2v6u_full_validation.pdf.gz | 428.6 KB | Display | |
Data in XML | 2v6u_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 2v6u_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v6/2v6u ftp://data.pdbj.org/pub/pdb/validation_reports/v6/2v6u | HTTPS FTP |
-Related structure data
Related structure data | 2v6sSC 2v6tC S: Starting model for refinement C: citing same article (ref.) |
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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: (-0.013, 0.954, -0.3), Vector: |
-Components
#1: Protein | Mass: 11953.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TOXOPLASMA GONDII (eukaryote) / Strain: RH / Plasmid: MODIFIED PET15B (NOVAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q2Q449, 4a-hydroxytetrahydrobiopterin dehydratase #2: Chemical | ChemComp-NA / | #3: 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: 3.22 Å3/Da / Density % sol: 64.5 % Description: PDB ENTRY 2V6S WAS USED AS A STARTING POINT FOR RIGID BODY REFINEMENT |
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Crystal grow | pH: 7.6 Details: 1.4 M AMMONIUM SULPHATE, 1 M LITHIUM SULPHATE, pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0064 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 17, 2006 / Details: MIRROR |
Radiation | Monochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0064 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→53.8 Å / Num. obs: 47707 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 9.2 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.8 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 5.8 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2V6S Resolution: 1.6→53.76 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.981 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.067 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→53.76 Å
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Refine LS restraints |
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