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Yorodumi- PDB-2h11: Amino-terminal Truncated Thiopurine S-Methyltransferase Complexed... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h11 | ||||||
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Title | Amino-terminal Truncated Thiopurine S-Methyltransferase Complexed with S-Adenosyl-L-Homocysteine | ||||||
Components | Thiopurine S-methyltransferase | ||||||
Keywords | TRANSFERASE / binary protein-cofactor complex | ||||||
Function / homology | Function and homology information Defective TPMT causes TPMT deficiency / thiopurine S-methyltransferase / thiopurine S-methyltransferase activity / xenobiotic metabolic process => GO:0006805 / Methylation / S-adenosyl-L-methionine binding / nucleobase-containing compound metabolic process / Azathioprine ADME / xenobiotic catabolic process / xenobiotic metabolic process ...Defective TPMT causes TPMT deficiency / thiopurine S-methyltransferase / thiopurine S-methyltransferase activity / xenobiotic metabolic process => GO:0006805 / Methylation / S-adenosyl-L-methionine binding / nucleobase-containing compound metabolic process / Azathioprine ADME / xenobiotic catabolic process / xenobiotic metabolic process / methylation / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Horton, J.R. / Cheng, X. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: Structural basis of allele variation of human thiopurine-S-methyltransferase. Authors: Wu, H. / Horton, J.R. / Battaile, K. / Allali-Hassani, A. / Martin, F. / Zeng, H. / Loppnau, P. / Vedadi, M. / Bochkarev, A. / Plotnikov, A.N. / Cheng, X. | ||||||
History |
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Remark 999 | SEQUENCE Residues 1-16 are deleted. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h11.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h11.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 2h11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h11_validation.pdf.gz | 595.4 KB | Display | wwPDB validaton report |
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Full document | 2h11_full_validation.pdf.gz | 622.8 KB | Display | |
Data in XML | 2h11_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2h11_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h1/2h11 ftp://data.pdbj.org/pub/pdb/validation_reports/h1/2h11 | HTTPS FTP |
-Related structure data
Related structure data | 2bzgSC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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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Components on special symmetry positions |
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Details | protein and product cofactor |
-Components
#1: Protein | Mass: 26646.660 Da / Num. of mol.: 2 / Fragment: amino-terminal truncated TPMT / Mutation: deleted residues 1-16 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TPMT / Plasmid: pGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O43213, UniProt: P51580*PLUS, thiopurine S-methyltransferase #2: Chemical | ChemComp-SCN / #3: Chemical | #4: Chemical | #5: 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: 2.42 Å3/Da / Density % sol: 49.24 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 30% PEG3350, 200mM potassium thiocyanate, 100mM buffer Bis-tris propane pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2005 |
Radiation | Monochromator: SAGITTALLY FOCUSED Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→33.58 Å / Num. all: 40680 / Num. obs: 40150 / % possible obs: 98.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.134 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.89→1.94 Å / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB: 2BZG Resolution: 1.89→33.58 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.89→33.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.94 Å / Rfactor Rfree error: 0.02
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