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Yorodumi- PDB-3aoe: Crystal structure of hetero-hexameric glutamate dehydrogenase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3aoe | ||||||
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Title | Crystal structure of hetero-hexameric glutamate dehydrogenase from Thermus thermophilus (Leu bound form) | ||||||
Components | (Glutamate dehydrogenase) x 2 | ||||||
Keywords | OXIDOREDUCTASE / Rossmann fold / glutamate dehydrogenase / dehydrogenase / NADH | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / glutamate dehydrogenase [NAD(P)+] activity / amino acid metabolic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
Citation | Journal: To be Published Title: An unique allosteric regulation revealed by hetero-hexameric glutamate dehydrogenase from Thermus thermophilus Authors: Tomita, T. / Kuzuyama, T. / Nishiyama, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3aoe.cif.gz | 914.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3aoe.ent.gz | 769 KB | Display | PDB format |
PDBx/mmJSON format | 3aoe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/3aoe ftp://data.pdbj.org/pub/pdb/validation_reports/ao/3aoe | HTTPS FTP |
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-Related structure data
Related structure data | 1b26S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 46168.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: gdhB, TT_C1211 / Plasmid: pET-gdhA/gdhB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q72IC1, glutamate dehydrogenase [NAD(P)+] #2: Protein | Mass: 44615.176 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / Gene: gdhA, TT_C1212 / Plasmid: pET-gdhA/gdhB / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q72IC0, glutamate dehydrogenase [NAD(P)+] #3: Chemical | ChemComp-LEU / #4: 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: 2.6 Å3/Da / Density % sol: 52.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate tribasic (pH5.6), 1.0M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2010 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30.22 Å / Num. all: 87634 / Num. obs: 87634 / % possible obs: 99.9 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 |
Reflection shell | Resolution: 2.6→2.64 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B26 Resolution: 2.6→30.22 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 24.844 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.944 / ESU R Free: 0.331 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.615 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→30.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.599→2.666 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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