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Yorodumi- PDB-1hdg: THE CRYSTAL STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hdg | ||||||
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Title | THE CRYSTAL STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM THE HYPERTHERMOPHILIC BACTERIUM THERMOTOGA MARITIMA AT 2.5 ANGSTROMS RESOLUTION | ||||||
Components | HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE (ALDEHY(D)-NAD(A)) | ||||||
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 / cytoplasm Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Korndoerfer, I. / Steipe, B. / Huber, R. / Tomschy, A. / Jaenicke, R. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: The crystal structure of holo-glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic bacterium Thermotoga maritima at 2.5 A resolution. Authors: Korndorfer, I. / Steipe, B. / Huber, R. / Tomschy, A. / Jaenicke, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hdg.cif.gz | 142.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hdg.ent.gz | 113.4 KB | Display | PDB format |
PDBx/mmJSON format | 1hdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hdg_validation.pdf.gz | 541.5 KB | Display | wwPDB validaton report |
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Full document | 1hdg_full_validation.pdf.gz | 550.2 KB | Display | |
Data in XML | 1hdg_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 1hdg_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/1hdg ftp://data.pdbj.org/pub/pdb/validation_reports/hd/1hdg | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36341.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TN10 / Plasmid: PAT1 GENE: TN10 References: UniProt: P17721, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % | ||||||||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 55 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: vapor diffusion | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 28069 / % possible obs: 99.7 % |
Reflection | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 128503 / Rmerge(I) obs: 0.054 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 41.4 % / Rmerge(I) obs: 0.139 |
-Processing
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Refinement | Resolution: 2.5→8 Å / σ(F): 2
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Displacement parameters | Biso mean: 21.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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