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Yorodumi- PDB-5jdw: CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jdw | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH GLYCINE | ||||||
Components | PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE) | ||||||
Keywords | TRANSFERASE / CREATINE BIOSYNTHESIS / CATALYTIC TRIAD / REACTION MECHANISM / NOVEL FOLD / FIVEFOLD PSEUDOSYMMETRY | ||||||
Function / homology | Function and homology information glycine amidinotransferase / glycine amidinotransferase activity / amidinotransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / muscle atrophy / mitochondrial intermembrane space / positive regulation of cold-induced thermogenesis / mitochondrial inner membrane ...glycine amidinotransferase / glycine amidinotransferase activity / amidinotransferase activity / creatine metabolic process / Creatine metabolism / creatine biosynthetic process / muscle atrophy / mitochondrial intermembrane space / positive regulation of cold-induced thermogenesis / mitochondrial inner membrane / learning or memory / mitochondrion / extracellular exosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.6 Å | ||||||
Authors | Fritsche, E. / Humm, A. / Huber, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: The ligand-induced structural changes of human L-Arginine:Glycine amidinotransferase. A mutational and crystallographic study. Authors: Fritsche, E. / Humm, A. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jdw.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jdw.ent.gz | 82.9 KB | Display | PDB format |
PDBx/mmJSON format | 5jdw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jdw ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jdw | HTTPS FTP |
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-Related structure data
Related structure data | 1jdxC 2jdxC 6jdwC 7jdwC 8jdwC 9jdwC 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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-Components
#1: Protein | Mass: 44341.488 Da / Num. of mol.: 1 / Fragment: RESIDUES 38 - 423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: BL(21)DE3PLYSS / Cellular location: CYTOSOLICCytosol / Gene: AT38H / Organ: KIDNEY / Organelle: MITOCHONDRIAMitochondrion / Plasmid: PRSETAT38H / Gene (production host): AT38H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P50440, glycine amidinotransferase |
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#2: Chemical | ChemComp-GLY / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.83 Å3/Da / Density % sol: 68 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7 / Details: pH 7.0 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: drop was made of a 7 micro litter protein solution and 14 micro litter of a reservoir solution | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→20 Å / Num. obs: 20930 / % possible obs: 93.7 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.115 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.6→8 Å / Cross valid method: FREE R / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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