+Open data
-Basic information
Entry | Database: PDB / ID: 1u1h | ||||||
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Title | A. thaliana cobalamine independent methionine synthase | ||||||
Components | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | ||||||
Keywords | TRANSFERASE / METHIONINE / SYNTHASE / HOMOCYSTEINE / METHYLTETRAHYDROFOLATE | ||||||
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 / plasmodesma / apoplast / plant-type vacuole / DNA methylation-dependent heterochromatin formation / methionine biosynthetic process ...: / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine synthase activity / 'de novo' L-methionine biosynthetic process / plasmodesma / apoplast / plant-type vacuole / DNA methylation-dependent heterochromatin formation / methionine biosynthetic process / chloroplast stroma / response to zinc ion / chloroplast / peroxisome / methylation / copper ion binding / mRNA binding / zinc ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å | ||||||
Authors | Ferrer, J.-L. / Ravanel, S. / Robert, M. / Dumas, R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Crystal structures of cobalamin-independent methionine synthase complexed with zinc, homocysteine, and methyltetrahydrofolate Authors: Ferrer, J.-L. / Ravanel, S. / Robert, M. / Dumas, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u1h.cif.gz | 159.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u1h.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 1u1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/1u1h ftp://data.pdbj.org/pub/pdb/validation_reports/u1/1u1h | HTTPS FTP |
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-Related 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: 85367.602 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CIMS / Plasmid: PET-MS1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: O50008, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MET / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% (W/V) POLY-ETHYLENE GLYCOL (PEG) 8000, 0.2 M AMMONIUM SULFATE, 1 MM DTT AND 0.1 M SODIUM CACODYLATE, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9792 / Wavelength: 0.9792 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 12, 2004 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→30 Å / Num. all: 71418 / Num. obs: 68990 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.2 Å2 / Rsym value: 0.088 / Net I/σ(I): 10.295 |
Reflection shell | Resolution: 2.56→2.62 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.081 / Rsym value: 0.391 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.55→29.61 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 427157.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 49.0365 Å2 / ksol: 0.332315 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→29.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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