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Yorodumi- PDB-1gxz: crystal structure of the eukaryotic mono-ADP-ribosyltransferase A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gxz | ||||||
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Title | crystal structure of the eukaryotic mono-ADP-ribosyltransferase ART2.2; Crystal form B (P212121) | ||||||
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 / NAD+ nucleosidase activity / hydrolase activity, acting on glycosyl bonds / NAD+ nucleotidase, cyclic ADP-ribose generating / NAD+-protein poly-ADP-ribosyltransferase activity / side of membrane / nucleotidyltransferase activity / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gxz.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gxz.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 1gxz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gxz_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
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Full document | 1gxz_full_validation.pdf.gz | 449.1 KB | Display | |
Data in XML | 1gxz_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 1gxz_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gx/1gxz ftp://data.pdbj.org/pub/pdb/validation_reports/gx/1gxz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99933, 0.01574, 0.03303), 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 48 % | |||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.02→33 Å / Num. obs: 30925 / % possible obs: 99.1 % / Redundancy: 4.1 % / Biso Wilson estimate: 8.4 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 2.02→2.13 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.177 / % possible all: 99.1 |
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 33 Å / Num. measured all: 126778 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 99.1 % / Num. unique obs: 4218 / Rmerge(I) obs: 0.18 |
-Processing
Software | Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→33 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.19 Å2 / ksol: 0.36 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 33 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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