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Yorodumi- PDB-3mtg: Crystal structure of human S-adenosyl homocysteine hydrolase-like... -
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-Basic information
Entry | Database: PDB / ID: 3mtg | ||||||
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Title | Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein | ||||||
Components | Putative adenosylhomocysteinase 2 | ||||||
Keywords | HYDROLASE / alpha/beta domain / tetramer / catalytic domain / co-factor binding domain / NAD / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information regulation of monoatomic ion transmembrane transporter activity / epithelial fluid transport / DAG and IP3 signaling / regulation of mRNA 3'-end processing / S-adenosylmethionine cycle / PLC beta mediated events / positive regulation of sodium ion transport / CLEC7A (Dectin-1) induces NFAT activation / : / regulation of cardiac conduction ...regulation of monoatomic ion transmembrane transporter activity / epithelial fluid transport / DAG and IP3 signaling / regulation of mRNA 3'-end processing / S-adenosylmethionine cycle / PLC beta mediated events / positive regulation of sodium ion transport / CLEC7A (Dectin-1) induces NFAT activation / : / regulation of cardiac conduction / Role of phospholipids in phagocytosis / Ion homeostasis / protein export from nucleus / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / regulation of monoatomic anion transport / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / Regulation of insulin secretion / angiotensin-activated signaling pathway / response to calcium ion / one-carbon metabolic process / apical plasma membrane / endoplasmic reticulum membrane / RNA binding / extracellular exosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å | ||||||
Authors | Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of human S-adenosyl homocysteine hydrolase-like 1 protein Authors: Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / ...Authors: Wisniewska, M. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nordlund, P. / Nyman, T. / Persson, C. / Schutz, P. / Thorsell, A.G. / Tresaugues, L. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Welin, M. / Schuler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mtg.cif.gz | 351.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mtg.ent.gz | 290.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mtg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/3mtg ftp://data.pdbj.org/pub/pdb/validation_reports/mt/3mtg | HTTPS FTP |
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-Related structure data
Related structure data | 3gvpS 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: 49476.805 Da / Num. of mol.: 2 / Fragment: SAHH-like domain (unp residues 89:530) / Mutation: T508A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AHCYL1, DCAL, Irbit, XPVKONA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) R3 pRARE / References: UniProt: O43865, adenosylhomocysteinase #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: 2.64 Å3/Da / Density % sol: 53.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M tri-sodium citrate dehydrate, 18% PEG 3350,0.1 M CHES, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MX-225 / Detector: CCD / Date: Nov 26, 2009 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→46.625 Å / Num. obs: 30565 / Redundancy: 7.7 % / Biso Wilson estimate: 69.89 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 |
Reflection shell | Resolution: 2.64→2.78 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.414 / Rsym value: 0.414 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3gvp Resolution: 2.64→33.59 Å / Cor.coef. Fo:Fc: 0.9165 / Cor.coef. Fo:Fc free: 0.8688 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 83.62 Å2
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Refine analyze | Luzzati coordinate error obs: 1.018 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→33.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.64→2.73 Å / Total num. of bins used: 15
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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