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Yorodumi- PDB-1xr2: Crystal Structure of oxidized T. maritima Cobalamin-Independent M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xr2 | ||||||
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Title | Crystal Structure of oxidized T. maritima Cobalamin-Independent Methionine Synthase complexed with Methyltetrahydrofolate | ||||||
Components | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | ||||||
Keywords | TRANSFERASE / TIM barrel / zinc / homocysteine / methyltetrahydrofolate | ||||||
Function / homology | Function and homology information 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / 'de novo' L-methionine biosynthetic process / methylation / zinc ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 | 1xr2.cif.gz | 288.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xr2.ent.gz | 237.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/1xr2 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/1xr2 | HTTPS FTP |
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-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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Details | The asymmetric unit contains two biological molecules |
-Components
#1: Protein | Mass: 89339.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: metE / Plasmid: PET151D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STAR References: UniProt: Q9X112, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase #2: Chemical | #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: 2.33 Å3/Da / Density % sol: 47.79 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor batch, under oil / pH: 5.2 Details: PEG 4000, SODIUM ACETATE, AMMONIUM SULFATE, pH 5.2, VAPOR BATCH, UNDER OIL, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||
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 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→19.95 Å / Num. all: 71086 / Num. obs: 69289 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.84 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.54 |
Reflection shell | Resolution: 2.35→2.54 Å / Redundancy: 4.54 % / Mean I/σ(I) obs: 4.5 / Num. unique all: 10923 / Rsym value: 0.331 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→19.95 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3776464.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.5336 Å2 / ksol: 0.325769 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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