+Open data
-Basic information
Entry | Database: PDB / ID: 1umy | ||||||
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Title | BHMT from rat liver | ||||||
Components | Betaine--homocysteine S-methyltransferase 1 | ||||||
Keywords | TRANSFERASE / METHIONINE SYNTHESIS / HOMOCYSTEINE METABOLISM / BETAINE / METHYLTRANSFERASE / ZINC | ||||||
Function / homology | Function and homology information Choline catabolism / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / Sulfur amino acid metabolism / amino-acid betaine catabolic process / 'de novo' L-methionine biosynthetic process / methionine biosynthetic process / methyltransferase activity ...Choline catabolism / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / Sulfur amino acid metabolism / amino-acid betaine catabolic process / 'de novo' L-methionine biosynthetic process / methionine biosynthetic process / methyltransferase activity / methylation / protein-containing complex binding / protein-containing complex / extracellular exosome / zinc ion binding / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Gonzalez, B. / Pajares, M.A. / Sanz-Aparicio, J. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2004 Title: Crystal structure of rat liver betaine homocysteine s-methyltransferase reveals new oligomerization features and conformational changes upon substrate binding. Authors: Gonzalez, B. / Pajares, M.A. / Martinez-Ripoll, M. / Blundell, T.L. / Sanz-Aparicio, J. #1: Journal: Biochem.J. / Year: 2003 Title: Active-Site Mutagenesis Study of Rat Liver Betaine Homocysteine S-Methyltransferase Authors: Gonzalez, B. / Garrido, F. / Gasset, M. / Sanz-Aparicio, J. / Pajares, M.A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Crystallization and Preliminary X-Ray Study of Recombinant Betaine-Homocysteine S-Methyltransferase from Rat Liver Authors: Gonzalez, B. / Pajares, M.A. / Too, P. / Garrido, F. / Blundell, T.L. / Sanz-Aparicio, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1umy.cif.gz | 309.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1umy.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 1umy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1umy_validation.pdf.gz | 488.3 KB | Display | wwPDB validaton report |
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Full document | 1umy_full_validation.pdf.gz | 590.2 KB | Display | |
Data in XML | 1umy_validation.xml.gz | 72.7 KB | Display | |
Data in CIF | 1umy_validation.cif.gz | 99.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/1umy ftp://data.pdbj.org/pub/pdb/validation_reports/um/1umy | HTTPS FTP |
-Related structure data
Related structure data | 1lt8S 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 45055.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: ZN BOUND FORM / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bhmt / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O09171, betaine-homocysteine S-methyltransferase #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE REGULATION OF HOMOCYSTEINE METABOLISM. CONVERTS HOMOCYSTEINE AND BETAINE TO ...INVOLVED IN THE REGULATION | |
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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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | pH: 8.5 / Details: 16% PEG 1500, PH=8.5, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.004 |
Detector | Detector: CCD / Date: Apr 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.004 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49 Å / Num. obs: 58532 / % possible obs: 99.7 % / Observed criterion σ(I): 4 / Redundancy: 4 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.5→2.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LT8 Resolution: 2.5→48.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT / Bsol: 61.82 Å2 / ksol: 0.356894 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→48.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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Xplor file |
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