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- PDB-3jdw: CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jdw | ||||||
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Title | CRYSTAL STRUCTURE AND MECHANISM OF L-ARGININE: GLYCINE AMIDINOTRANSFERASE: A MITOCHONDRIAL ENZYME INVOLVED IN CREATINE BIOSYNTHESIS | ||||||
![]() | 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 | ![]() | ||||||
![]() | Humm, A. / Fritsche, E. / Steinbacher, S. / Huber, R. | ||||||
![]() | ![]() Title: Crystal structure and mechanism of human L-arginine:glycine amidinotransferase: a mitochondrial enzyme involved in creatine biosynthesis. Authors: Humm, A. / Fritsche, E. / Steinbacher, S. / Huber, R. #1: ![]() Title: Structure and Reaction Mechanism of L-Arginine:Glycine Amidinotransferase Authors: Humm, A. / Fritsche, E. / Steinbacher, S. #2: ![]() Title: Substrate Binding and Catalysis by L-Arginine:Glycine Amidinotransferase--A Mutagenesis and Crystallographic Study Authors: Fritsche, E. / Humm, A. / Huber, R. #3: ![]() Title: Recombinant Expression and Isolation of Human L-Arginine:Glycine Amidinotransferase and Identification of its Active-Site Cysteine Residue Authors: Humm, A. / Fritsche, E. / Mann, K. / Gohl, M. / Huber, R. #4: ![]() Title: Bioincorporation of Telluromethionine Into Proteins: A Promising New Approach for X-Ray Structure Analysis of Proteins Authors: Budisa, N. / Karnbrock, W. / Steinbacher, S. / Humm, A. / Prade, L. / Neuefeind, T. / Moroder, L. / 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 | ![]() | 111.1 KB | Display | ![]() |
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PDB format | ![]() | 86.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 380.2 KB | Display | ![]() |
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Full document | ![]() | 383.5 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jdwSC ![]() 2jdwC ![]() 4jdwC S: Starting model for refinement 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: 48521.367 Da / Num. of mol.: 1 / Fragment: RESIDUES 64 - 423 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Description: WITHOUT SIGNAL SEQUENCE (1-37) BUT WITH N-TERMINAL ATTACHED 6-HISTIDINE-TAG (14 RESIDUES) Cell line: BL21 Cellular location: INTERMEMBRANE SPACE OF MITOCHONDRIA AND CYTOPLASM Gene: AT38H / Organ: KIDNEY / Organelle: MITOCHONDRIA / Plasmid: PRSETAT38H / Cellular location (production host): CYTOSOLIC / Gene (production host): AT38H / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ORN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7 Details: 1 PART OF AT38H (13-16 MG/ML) 2 PARTS OF PRECIPITANT (3% PEG 6000, 40 MM HEPES, 1MM GLUTATHIONE, PH7.0), SEVERAL DAYS AT ROOM TEMPERATURE, MACRO SEEDING. Temp details: room temp | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 290 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 11, 1995 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→8 Å / Num. obs: 25838 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 3.78 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.4→2.43 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.287 / % possible all: 51.9 |
Reflection shell | *PLUS % possible obs: 51.9 % |
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Processing
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Refinement | Method to determine structure: ISOMORPHOUS WITH PDB ENTRY 1JDW Starting model: PDB ENTRY 1JDW Resolution: 2.4→8 Å / Cross valid method: FREE R / σ(F): 0 Details: RESIDUES 38 - 63 ARE NOT VISIBLE IN THE ELECTRON DENSITY
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Displacement parameters | Biso mean: 27.61 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.43 Å / Total num. of bins used: 30
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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