[English] 日本語
Yorodumi- PDB-1gxy: crystal structure of the eucaryotic mono-ADP-ribosyltransferase A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxy | ||||||
---|---|---|---|---|---|---|---|
Title | crystal structure of the eucaryotic mono-ADP-ribosyltransferase ART2.2; CRYSTAL FORM A (P21) | ||||||
Components | T-CELL ECTO-ADP-RIBOSYLTRANSFERASE 2 | ||||||
Keywords | TRANSFERASE / ADP-RIBOSYLTRANSFERASE / IMMUNO-REGULATION | ||||||
Function / homology | Function and homology information : / NAD+ glycohydrolase / NAD+-protein-arginine ADP-ribosyltransferase / NAD+-protein-arginine ADP-ribosyltransferase activity / NAD catabolic process / hydrolase activity, acting on glycosyl bonds / NAD+ ADP-ribosyltransferase activity / side of membrane / nucleotidyltransferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.71 Å | ||||||
Authors | Mueller-Dieckmann, C. / Schulz, G.E. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Structure of the Ecto-Adp-Ribosyl Transferase Art2.2 From Rat Authors: Mueller-Dieckmann, C. / Ritter, H. / Haag, F. / Koch-Nolte, F. / Schulz, G.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1gxy.cif.gz | 108.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1gxy.ent.gz | 88.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxy ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxy | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.12554, 0.02431, -0.99179), Vector: |
-Components
#1: Protein | Mass: 26068.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM522 References: UniProt: P20974, NAD+-protein-arginine ADP-ribosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8.3 Details: 100 MM TRIS PH8.3, 200 MM LI2SO4, 22 % PEG4000, pH 8.30 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, hanging dropDetails: Mueller-Dieckmann, C., (2002) Acta Crystallogr., D58, 1211. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9094 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9094 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→29 Å / Num. obs: 48705 / % possible obs: 99.1 % / Redundancy: 4 % / Biso Wilson estimate: 17.5 Å2 / Rsym value: 0.034 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.71→1.8 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 6 / Rsym value: 0.119 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 29 Å / Num. measured all: 195638 / Rmerge(I) obs: 0.034 |
Reflection shell | *PLUS % possible obs: 99.1 % / Num. unique obs: 6787 / Rmerge(I) obs: 0.119 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS / Resolution: 1.71→29 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.77 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→29 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.71→1.82 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 35 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.223 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|