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Yorodumi- PDB-3ffs: The Crystal Structure of Cryptosporidium parvum Inosine-5'-Monoph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ffs | ||||||
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Title | The Crystal Structure of Cryptosporidium parvum Inosine-5'-Monophosphate Dehydrogenase | ||||||
Components | Inosine-5-monophosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / beta-alpha barrel / TIM fold | ||||||
Function / homology | Function and homology information IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Cryptosporidium parvum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.19 Å | ||||||
Authors | Riera, T.V. / D'Aquino, J.A. / Lu, J. / Petsko, G.A. / Hedstrom, L. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: The structural basis of Cryptosporidium -specific IMP dehydrogenase inhibitor selectivity Authors: Macpherson, I.S. / Kirubakaran, S. / Gorla, S.K. / Riera, T.V. / D'Aquino, J.A. / Zhang, M. / Cuny, G.D. / Hedstrom, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ffs.cif.gz | 221.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ffs.ent.gz | 175.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ffs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ffs_validation.pdf.gz | 462.3 KB | Display | wwPDB validaton report |
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Full document | 3ffs_full_validation.pdf.gz | 490.3 KB | Display | |
Data in XML | 3ffs_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 3ffs_validation.cif.gz | 57.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ff/3ffs ftp://data.pdbj.org/pub/pdb/validation_reports/ff/3ffs | HTTPS FTP |
-Related structure data
Related structure data | 3khjC 1eepS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 3 - 378 / Label seq-ID: 3 - 378
NCS ensembles :
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-Components
#1: Protein | Mass: 43134.262 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: IMPDH, 56k.02 / Plasmid: pTacTac / Production host: Escherichia coli (E. coli) / Strain (production host): TX685 / References: UniProt: Q8T6T2, IMP dehydrogenase |
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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: 2.6 Å3/Da / Density % sol: 52.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Protein solution: 4 mg/mL IMPDH, 50 mM Tris, pH 7.5, 150 mM KCl, 5 % glycerol and 2 mM dithiothreitol. Well solution: 34 % PEG 4000, 25 mM sodium acetate and 100 mM Tris-Cl, pH 8.5. Combined ...Details: Protein solution: 4 mg/mL IMPDH, 50 mM Tris, pH 7.5, 150 mM KCl, 5 % glycerol and 2 mM dithiothreitol. Well solution: 34 % PEG 4000, 25 mM sodium acetate and 100 mM Tris-Cl, pH 8.5. Combined in a 1:1 ratio. VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 8-BM / Wavelength: 0.97946 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2006 |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.19→50 Å / Num. obs: 30575 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.179 / Χ2: 1.171 |
Reflection shell | Resolution: 3.19→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.632 / Num. unique all: 2987 / Χ2: 1.072 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1EEP Resolution: 3.19→48.34 Å / Cor.coef. Fo:Fc: 0.866 / Cor.coef. Fo:Fc free: 0.82 / WRfactor Rfree: 0.313 / WRfactor Rwork: 0.259 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.953 / SU B: 26.148 / SU ML: 0.45 / SU Rfree: 0.58 / Cross valid method: THROUGHOUT / ESU R Free: 0.58 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.19 Å2 / Biso mean: 53.887 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: LAST / Resolution: 3.19→48.34 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 1614 / Refine-ID: X-RAY DIFFRACTION
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