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Yorodumi- PDB-1t7l: Crystal Structure of Cobalamin-Independent Methionine Synthase fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t7l | ||||||
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Title | Crystal Structure of Cobalamin-Independent Methionine Synthase from T. maritima | ||||||
Components | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | ||||||
Keywords | TRANSFERASE / TIM BARREL / HOMOCYSTEINE / METHYLTETRAHYDROFOLATE / ZINC | ||||||
Function / homology | Function and homology information 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine synthase activity / 'de novo' L-methionine biosynthetic process / methylation / zinc ion binding / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pejchal, R. / Ludwig, M.L. | ||||||
Citation | Journal: Plos Biol. / Year: 2005 Title: Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication Authors: Pejchal, R. / 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 | 1t7l.cif.gz | 306.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t7l.ent.gz | 251.8 KB | Display | PDB format |
PDBx/mmJSON format | 1t7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1t7l_validation.pdf.gz | 469 KB | Display | wwPDB validaton report |
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Full document | 1t7l_full_validation.pdf.gz | 490.4 KB | Display | |
Data in XML | 1t7l_validation.xml.gz | 57.2 KB | Display | |
Data in CIF | 1t7l_validation.cif.gz | 81 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/1t7l ftp://data.pdbj.org/pub/pdb/validation_reports/t7/1t7l | 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: 89410.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: METE, TM1286 / Plasmid: PET-151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) References: UniProt: Q9X112, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase #2: Chemical | #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: 2.33 Å3/Da / Density % sol: 47.2 % |
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Crystal grow | Temperature: 295 K / Method: vapor batch, under oil / pH: 4.6 Details: PEG 4000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR BATCH, UNDER OIL, temperature 295.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 22, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.91 Å / Num. all: 112572 / Num. obs: 112572 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.081 / Net I/σ(I): 13.77 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 4.35 / Num. unique all: 14848 / Rsym value: 0.381 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3599544.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: molecular replacement model derived from experimental model based on Se SAD phases
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48.9798 Å2 / ksol: 0.363465 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→19.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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