+Open data
-Basic information
Entry | Database: PDB / ID: 1l1f | ||||||
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Title | Structure of human glutamate dehydrogenase-apo form | ||||||
Components | Glutamate Dehydrogenase 1 | ||||||
Keywords | OXIDOREDUCTASE / Allostery / negative cooperativity | ||||||
Function / homology | Function and homology information L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate biosynthetic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamine metabolic process ...L-leucine binding / glutamate dehydrogenase [NAD(P)+] activity / glutamate catabolic process / glutamate biosynthetic process / tricarboxylic acid metabolic process / glutamate dehydrogenase [NAD(P)+] / glutamate dehydrogenase (NADP+) activity / glutamate dehydrogenase (NAD+) activity / Glutamate and glutamine metabolism / glutamine metabolic process / NAD+ binding / substantia nigra development / ADP binding / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / mitochondrial matrix / GTP binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Smith, T.J. / Schmidt, T. / Fang, J. / Wu, J. / Siuzdak, G. / Stanley, C.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: The structure of apo human glutamate dehydrogenase details subunit communication and allostery. Authors: Smith, T.J. / Schmidt, T. / Fang, J. / Wu, J. / Siuzdak, G. / Stanley, C.A. | ||||||
History |
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Remark 400 | COMPOUND NAD binding domain orientation differs among the six chains. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1l1f.cif.gz | 555.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1l1f.ent.gz | 465.6 KB | Display | PDB format |
PDBx/mmJSON format | 1l1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/1l1f ftp://data.pdbj.org/pub/pdb/validation_reports/l1/1l1f | HTTPS FTP |
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-Related structure data
Related structure data | 1hwx |
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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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-Components
#1: Protein | Mass: 56085.566 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) References: UniProt: P00367, glutamate dehydrogenase [NAD(P)+] |
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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: 2.89 Å3/Da / Density % sol: 57.49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: PEG 8000, NaCl, sodium phosphate, sodium azide, octyl-b-glucopyranoside, methyl pentanediol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 14, 2001 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→30 Å / Num. all: 94574 / Num. obs: 91356 / % possible obs: 90.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rsym value: 0.047 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. obs: 94574 / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 2.82 Å / % possible obs: 54.8 % / Num. unique obs: 7168 / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Software | *PLUS Name: 0 / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 8 Å / σ(F): 2 / Num. reflection Rfree: 30 / % reflection Rfree: 5 % / Rfactor obs: 0.262 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |