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Yorodumi- PDB-1j0x: Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j0x | ||||||
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Title | Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH) | ||||||
Components | glyceraldehyde-3-phosphate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / dehydrogenase / Rossmann fold / mammalian GAPDH / apoptosis / negative cooperativity | ||||||
Function / homology | Function and homology information peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / glycolytic process / microtubule cytoskeleton organization / glucose metabolic process / NAD binding ...peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / glycolytic process / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / microtubule cytoskeleton / regulation of translation / NADP binding / microtubule binding / neuron apoptotic process / protein stabilization / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Cowan-Jacob, S.W. / Kaufmann, M. / Anselmo, A.N. / Stark, W. / Grutter, M.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structure of rabbit-muscle glyceraldehyde-3-phosphate dehydrogenase. Authors: Cowan-Jacob, S.W. / Kaufmann, M. / Anselmo, A.N. / Stark, W. / Grutter, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j0x.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j0x.ent.gz | 213.9 KB | Display | PDB format |
PDBx/mmJSON format | 1j0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1j0x_validation.pdf.gz | 1017 KB | Display | wwPDB validaton report |
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Full document | 1j0x_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1j0x_validation.xml.gz | 55.4 KB | Display | |
Data in CIF | 1j0x_validation.cif.gz | 75.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j0/1j0x ftp://data.pdbj.org/pub/pdb/validation_reports/j0/1j0x | HTTPS FTP |
-Related structure data
Related structure data | 1gd1S 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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Details | Chain O, P, Q, R form the biologically active tetramer |
-Components
#1: Protein | Mass: 35755.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) References: UniProt: P46406, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | #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: 2.48 Å3/Da / Density % sol: 50.04 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 3350, HEPES, K3-citrate, microseeding, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.8 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: Mirror |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→17.93 Å / Num. all: 58424 / Num. obs: 56521 / % possible obs: 96.6 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.034 |
Reflection shell | Resolution: 2.4→2.49 Å / % possible all: 86.1 |
Reflection | *PLUS Redundancy: 3.4 % / Num. measured all: 194719 / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS % possible obs: 86.1 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.227 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Dimer of PDB ENTRY 1GD1 Resolution: 2.4→17.93 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: torsion angle molecular dynamics simulated annealing maximum likelihood minimization individual B-factor refinement NCS-restraints. The structure was also refined with X-PLOR and CNX
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Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→17.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015
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Xplor file |
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