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Yorodumi- PDB-1qi6: SECOND APO FORM OF AN NADP DEPENDENT ALDEHYDE DEHYDROGENASE WITH ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qi6 | ||||||
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Title | SECOND APO FORM OF AN NADP DEPENDENT ALDEHYDE DEHYDROGENASE WITH GLU250 SITUATED 3.7 A FROM CYS284 | ||||||
Components | PROTEIN (NADP DEPENDENT NONPHOSPHORYLATING GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE) | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (NADP+) / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (non-phosphorylating) activity / lactaldehyde dehydrogenase (NAD+) activity / glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity Similarity search - Function | ||||||
Biological species | Streptococcus mutans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Cobessi, D. / Tete-Favier, F. / Marchal, S. / Branlant, G. / Aubry, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2000 Title: Structural and biochemical investigations of the catalytic mechanism of an NADP-dependent aldehyde dehydrogenase from Streptococcus mutans. Authors: Cobessi, D. / Tete-Favier, F. / Marchal, S. / Branlant, G. / Aubry, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qi6.cif.gz | 362 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qi6.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qi6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qi6_validation.pdf.gz | 399.1 KB | Display | wwPDB validaton report |
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Full document | 1qi6_full_validation.pdf.gz | 407.1 KB | Display | |
Data in XML | 1qi6_validation.xml.gz | 34.6 KB | Display | |
Data in CIF | 1qi6_validation.cif.gz | 55.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qi/1qi6 ftp://data.pdbj.org/pub/pdb/validation_reports/qi/1qi6 | HTTPS FTP |
-Related structure data
Related structure data | 1qi1C 1euhS 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 51276.438 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: SO4 / Source: (gene. exp.) Streptococcus mutans (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: Q59931, glyceraldehyde-3-phosphate dehydrogenase (NADP+) #2: Chemical | ChemComp-SO4 / #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: 2.98 Å3/Da / Density % sol: 60 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 2.0 M AMMONIUM SULPHATE, 2 % PEG 400, HEPES O.1 M PH 7.5, PROTEIN 5MG/ML, pH 8.5 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418 |
Detector | Type: ENRAF-NONIUS / Detector: IMAGE PLATE / Date: Jun 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 81791 / % possible obs: 96 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.059 / Rsym value: 0.059 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.188 / Rsym value: 0.188 / % possible all: 68.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EUH Resolution: 2.5→8 Å / Data cutoff high absF: 3500 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / σ(F): 0 / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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