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Yorodumi- PDB-1vsv: Crystal Structure of holo-glyceraldehyde 3-phosphate dehydrogenas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vsv | |||||||||
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Title | Crystal Structure of holo-glyceraldehyde 3-phosphate dehydrogenase from Cryptosporidium parvum | |||||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / dehyrogenase / glycolysis / glycolytic enzyme | |||||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Cryptosporidium parvum (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Cook, W.J. / Senkovich, O. / Chattopadhyay, D. | |||||||||
Citation | Journal: BMC STRUCT.BIOL. / Year: 2009 Title: An unexpected phosphate binding site in Glyceraldehyde 3-Phosphate Dehydrogenase: Crystal structures of apo, holo and ternary complex of Cryptosporidium parvum enzyme Authors: Cook, W.J. / Senkovich, O. / Chattopadhyay, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vsv.cif.gz | 270.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vsv.ent.gz | 219.1 KB | Display | PDB format |
PDBx/mmJSON format | 1vsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vsv_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1vsv_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1vsv_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 1vsv_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vsv ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vsv | HTTPS FTP |
-Related structure data
Related structure data | 1vsuSC 3cifC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38333.844 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q7YYQ9, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #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: 2.27 Å3/Da / Density % sol: 45.86 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 20% PEG 3000, pH 7.5, vapor diffusion, hanging drop, temperature 298K, pH 7.50 |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9998 |
Detector | Type: MAR300 / Detector: CCD / Date: Jul 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9998 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 87612 / % possible obs: 98.3 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.7 Å2 / Rsym value: 0.068 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.3 % / Rsym value: 0.365 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VSU Resolution: 2→48.85 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2060261.67 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.5054 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→48.85 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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