+Open data
-Basic information
Entry | Database: PDB / ID: 8kao | ||||||
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Title | Glutamate dehydrogenase-69O | ||||||
Components | Glutamate dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / glutamate dehydrogenase | ||||||
Function / homology | Function and homology information glutamate dehydrogenase (NAD+) activity / glutamate catabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å | ||||||
Authors | Sakuraba, H. / Ohshima, T. | ||||||
Funding support | 1items
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Citation | Journal: To be published Title: Structure of glutamate dehydrogenase-69O Authors: Sakuraba, H. / Ohshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kao.cif.gz | 236 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kao.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 8kao.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kao_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8kao_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8kao_validation.xml.gz | 44 KB | Display | |
Data in CIF | 8kao_validation.cif.gz | 61.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ka/8kao ftp://data.pdbj.org/pub/pdb/validation_reports/ka/8kao | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 45561.473 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (archaea) / Gene: HFC64_02080 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0E3K1C8 #2: Chemical | ChemComp-NAD / | #3: Chemical | ChemComp-69O / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.8 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 100 mM Potassium phosphate monobasic/Sodium phosphate dibasic buffer (pH 6.2), 10% (w/v) polyethylene glycol (PEG) 3,000, and 10% (v/v) glycerol. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→45.04 Å / Num. obs: 48864 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.068 / Rrim(I) all: 0.18 / Χ2: 0.98 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.55→2.63 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 1.164 / Num. measured all: 30810 / Num. unique obs: 4486 / CC1/2: 0.708 / Rpim(I) all: 0.476 / Rrim(I) all: 1.259 / Χ2: 1 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→45.04 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.32 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.55 / ESU R Free: 0.303 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.374 Å2
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Refinement step | Cycle: 1 / Resolution: 2.55→45.04 Å
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