+Open data
-Basic information
Entry | Database: PDB / ID: 3jud | ||||||
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Title | Human gamma-glutamylamine cyclotransferase, E82Q mutant | ||||||
Components | AIG2-like domain-containing protein 1 | ||||||
Keywords | TRANSFERASE / cyclotransferase / gamma-glutamylamine cyclotransferase / gamma-glutamyl-epsilon-lysine / Epsilon-(gamma-Glutamyl)-lysine / oxoproline / 5-oxo-L-proline / cyclotransferase fold / mutant | ||||||
Function / homology | Function and homology information gamma-glutamylamine cyclotransferase / cellular modified amino acid catabolic process / gamma-glutamylaminecyclotransferase activity / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å | ||||||
Authors | Oakley, A.J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Identification and characterization of {gamma}-glutamylamine cyclotransferase: An enzyme responsible for {gamma}-glutamyl-{epsilon}-lysine catabolism Authors: Oakley, A.J. / Coggan, M. / Board, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jud.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jud.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jud_validation.pdf.gz | 440.7 KB | Display | wwPDB validaton report |
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Full document | 3jud_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 3jud_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 3jud_validation.cif.gz | 16.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/3jud ftp://data.pdbj.org/pub/pdb/validation_reports/ju/3jud | HTTPS FTP |
-Related structure data
Related structure data | 3jubC 3jucC 1vkbS C: citing same article (ref.) S: Starting model for refinement |
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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: 17351.590 Da / Num. of mol.: 1 / Mutation: E82Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: A2LD1, GGACT / Plasmid: pHUE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BVM4, EC: 2.3.2.4 | ||
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#2: Chemical | #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: 1.88 Å3/Da / Density % sol: 34.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12.5%(w/v) PEG3350, 0.3M ammonium nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.826966 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2009 / Details: beamline optics |
Radiation | Monochromator: beamline optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826966 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→37.95 Å / Num. all: 74200 / Num. obs: 74200 / % possible obs: 97.7 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 6.7 % / Biso Wilson estimate: 5 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 0.98→1.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.5 / Num. unique all: 10958 / Rsym value: 0.688 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1VKB Resolution: 0.98→27.57 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.722 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.026 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.444 Å2
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Refinement step | Cycle: LAST / Resolution: 0.98→27.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 0.98→1.005 Å / Total num. of bins used: 20
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