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- PDB-7jdw: CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7jdw | |||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN L-ARGININE:GLYCINE AMIDINOTRANSFERASE IN COMPLEX WITH DELTA-AMINO VALERIC ACID | |||||||||
![]() | PROTEIN (L-ARGININE:GLYCINE AMIDINOTRANSFERASE) | |||||||||
![]() | TRANSFERASE / CREATINE BIOSYNTHESIS / CATALYTIC TRIAD / REACTION MECHANISM / NOVEL FOLD / FIVEFOLD PSEUDOSYMMETRY | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() | |||||||||
![]() | Fritsche, E. / Humm, A. / Huber, R. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 106.8 KB | Display | ![]() |
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PDB format | ![]() | 82.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 375.1 KB | Display | ![]() |
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Full document | ![]() | 380 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jdxC ![]() 2jdxC ![]() 5jdwC ![]() 6jdwC ![]() 8jdwC ![]() 9jdwC C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Description: WITHOUT SIGNAL SEQUENCE (1-37) BUT WURCE 19 N-TERMINAL ATTACHED 6-HISTIDINE- TAG (14 RESIDUES) Cellular location: CYTOSOLIC / Gene: AT38H / Organ: KIDNEY / Organelle: MITOCHONDRIA / Plasmid: PRSETAT38H / Gene (production host): AT38H / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-DAV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() |
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: 2.37→20 Å / Num. obs: 26463 / % possible obs: 90.4 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Rsym value: 0.105 |
Reflection | *PLUS Num. measured all: 113088 / Rmerge(I) obs: 0.105 |
Reflection shell | *PLUS % possible obs: 89.4 % / Rmerge(I) obs: 0.276 |
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Processing
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Refinement | Method to determine structure: OTHER / Resolution: 2.37→8 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.37→8 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |