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Yorodumi- PDB-1lt7: Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lt7 | ||||||
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Title | Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four Sm(III) ions | ||||||
Components | BETAINE-HOMOCYSTEINE METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE / homocysteine metabolism / homocysteinemia / thiol alkyl transfer | ||||||
Function / homology | Function and homology information regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation ...regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation / zinc ion binding / extracellular exosome / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å | ||||||
Authors | Evans, J.C. / Huddler, D.P. / Jiracek, J. / Castro, C. / Millian, N.S. / Garrow, T.A. / Ludwig, M.L. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Betaine-homocysteine methyltransferase: zinc in a distorted barrel. Authors: Evans, J.C. / Huddler, D.P. / Jiracek, J. / Castro, C. / Millian, N.S. / Garrow, T.A. / Ludwig, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lt7.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lt7.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lt7_validation.pdf.gz | 465.3 KB | Display | wwPDB validaton report |
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Full document | 1lt7_full_validation.pdf.gz | 491.8 KB | Display | |
Data in XML | 1lt7_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1lt7_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/1lt7 ftp://data.pdbj.org/pub/pdb/validation_reports/lt/1lt7 | 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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-Components
#1: Protein | Mass: 44844.020 Da / Num. of mol.: 2 / Mutation: P2A, C104A, C131A, C186A, C201A, C256A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 References: UniProt: Q93088, betaine-homocysteine S-methyltransferase #2: Chemical | ChemComp-SM / #3: Chemical | #4: 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: 2.08 Å3/Da / Density % sol: 40.96 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2 Details: PEG 200, sodium citrate, N,N-dimethylglycine, samarium (III) acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 5.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.845, 1.746 | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 12, 2002 | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.15→100 Å / Num. all: 78638 / Num. obs: 78638 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.88 % / Biso Wilson estimate: 40.2 Å2 / Limit h max: 51 / Limit h min: 0 / Limit k max: 41 / Limit k min: 0 / Limit l max: 34 / Limit l min: -41 / Observed criterion F max: 324855.27 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 17.3 | |||||||||
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.41 / Num. unique all: 7838 / Rsym value: 0.213 / % possible all: 99.9 | |||||||||
Reflection | *PLUS Lowest resolution: 50 Å / Num. obs: 40062 / Redundancy: 3.7 % / Num. measured all: 148174 | |||||||||
Reflection shell | *PLUS % possible obs: 99.9 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.15→9.99 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 100.343 Å2 / ksol: 0.491514 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.17 Å2 / Biso mean: 36.79 Å2 / Biso min: 11.7 Å2
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Refine Biso |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→9.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.248 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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