+Open data
-Basic information
Entry | Database: PDB / ID: 2vyv | ||||||
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Title | Structure of E.Coli GAPDH Rat Sperm GAPDH heterotetramer | ||||||
Components | (GLYCERALDEHYDE-3-PHOSPHATE ...) x 2 | ||||||
Keywords | OXIDOREDUCTASE / CONTRACEPTIVE / ALPHA CHLOROHYDRIN / GLYCERALDEHYDE-3-PHOSPHATE / NAD / GAPDH / RAT SPERM / CYTOPLASM / GLYCOLYSIS | ||||||
Function / homology | Function and homology information Glycolysis / sperm fibrous sheath / sperm principal piece / Gluconeogenesis / flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / motile cilium / spermatid development / acrosomal vesicle ...Glycolysis / sperm fibrous sheath / sperm principal piece / Gluconeogenesis / flagellated sperm motility / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / motile cilium / spermatid development / acrosomal vesicle / glycolytic process / cilium / glucose metabolic process / NAD binding / NADP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI BL21 (bacteria) RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å | ||||||
Authors | Frayne, J. / Taylor, A. / Hall, L. / Hadfield, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Structure of Insoluble Rat Sperm Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) Via Heterotetramer Formation with Escherichia Coli Gapdh Reveals Target for Contraceptive Design. Authors: Frayne, J. / Taylor, A. / Cameron, G. / Hadfield, A.T. | ||||||
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 | 2vyv.cif.gz | 286.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vyv.ent.gz | 230.7 KB | Display | PDB format |
PDBx/mmJSON format | 2vyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vyv_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2vyv_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2vyv_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 2vyv_validation.cif.gz | 84.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/2vyv ftp://data.pdbj.org/pub/pdb/validation_reports/vy/2vyv | HTTPS FTP |
-Related structure data
Related structure data | 2vynC 2yvnS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-GLYCERALDEHYDE-3-PHOSPHATE ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 35641.434 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant: pLysS References: UniProt: P0A9B2, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Protein | | Mass: 36376.578 Da / Num. of mol.: 1 / Fragment: RESIDUES 102-432 / Source method: isolated from a natural source / Details: DNA WAS EXTRACTED DIRECTLY FROM RAT TESTIS / Source: (natural) RATTUS NORVEGICUS (Norway rat) / Tissue: TESTIS References: UniProt: Q9ESV6, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) |
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-Non-polymers , 4 types, 859 molecules
#3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-NAD / #5: Chemical | ChemComp-1GP / | #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: 2.1 Å3/Da / Density % sol: 42 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: 0.2M NA FORMATE, 20% PEG 3350, 0.1M HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 16, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→28.6 Å / Num. obs: 51658 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.38→2.43 Å / % possible all: 78.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2YVN Resolution: 2.38→28.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.925 / SU B: 9.862 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 1.19 / ESU R Free: 0.305 / 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: 34.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.38→28.62 Å
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