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Yorodumi- PDB-2gb4: Crystal structure of Thiopurine methyltransferase (18204406) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gb4 | ||||||
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Title | Crystal structure of Thiopurine methyltransferase (18204406) from Mus musculus at 1.35 A resolution | ||||||
Components | Thiopurine S-methyltransferase | ||||||
Keywords | TRANSFERASE / 18204406 / Thiopurine methyltransferase / Structural Genomics / PSI / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG | ||||||
Function / homology | Function and homology information thiopurine S-methyltransferase / thiopurine S-methyltransferase activity / Methylation / Azathioprine ADME / methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Thiopurine methyltransferase (18204406) from Mus musculus at 1.35 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2gb4.cif.gz | 223.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gb4.ent.gz | 177.7 KB | Display | PDB format |
PDBx/mmJSON format | 2gb4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2gb4_validation.pdf.gz | 992.4 KB | Display | wwPDB validaton report |
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Full document | 2gb4_full_validation.pdf.gz | 998.4 KB | Display | |
Data in XML | 2gb4_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 2gb4_validation.cif.gz | 34.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/2gb4 ftp://data.pdbj.org/pub/pdb/validation_reports/gb/2gb4 | HTTPS FTP |
-Related structure data
Related structure data | 2bzgS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 29086.346 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tpmt / Production host: Escherichia coli (E. coli) / References: UniProt: O55060, thiopurine S-methyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 48.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.6 Details: 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2005 | ||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→50 Å / Num. obs: 125498 / % possible obs: 79.4 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 15.4 | ||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2bzg Resolution: 1.25→35.9 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.925 / Num. parameters: 38290 / Num. restraintsaints: 50906 / SU B: 2.556 / SU ML: 0.059 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 8%. 3. THE NOMINAL RESOLUTION IS 1.35A WITH 16569 REFLECTIONS BETWEEN 1.35-1.25A ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 8%. 3. THE NOMINAL RESOLUTION IS 1.35A WITH 16569 REFLECTIONS BETWEEN 1.35-1.25A (50.6% COMPLETE FOR THIS SHELL) INCLUDED IN THIS REFINEMENT. 4. REFINEMENT WAS AGAINST INTENSITY DATA. 5. NCS RESTRAINTS WERE APPLIED BETWEEN RESIDUES 40-158, 162-186 AND 205-240 OF CHAINS A AND B. 6. RESIDUES 1-9 OF CHAIN A AND 1-10 OF CHAIN B HAVE NO DENSITY AND WERE NOT MODELED. 7. S-ADENOSYL-L-HOMOCYSTEINE MODELED BASED ON ELECTRON DENSITY AND PROPOSED FUNCTION. 8. DATA WAS REFINED WITH TWIN LAW -H, -K, H+L, TWIN FRACTION 0.50. 9. THE RFREE SET WAS GENERATED WITH THE TWIN LAW.
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.394 Å2
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Refine analyze | Num. disordered residues: 11 / Occupancy sum hydrogen: 3551 / Occupancy sum non hydrogen: 4169 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→35.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.249→1.282 Å / Total num. of bins used: 20
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