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Yorodumi- PDB-3iva: Structure of the B12-dependent Methionine Synthase (MetH) C-temin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iva | ||||||
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Title | Structure of the B12-dependent Methionine Synthase (MetH) C-teminal half with AdoHcy bound | ||||||
Components | Methionine synthase | ||||||
Keywords | TRANSFERASE / METH / reactivation conformation / H759 / cobalamin / intermodular interactions / amino-acid biosynthesis / cobalt / metal-binding / methionine biosynthesis / methyltransferase / S-adenosyl-L-methionine / S-adenosyl-homocysteine | ||||||
Function / homology | Function and homology information methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methylation / zinc ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Pattridge, K.A. / Koutmos, M. / Smith, J.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Insights into the reactivation of cobalamin-dependent methionine synthase. Authors: Koutmos, M. / Datta, S. / Pattridge, K.A. / Smith, J.L. / Matthews, R.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iva.cif.gz | 134.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iva.ent.gz | 101.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iva.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/3iva ftp://data.pdbj.org/pub/pdb/validation_reports/iv/3iva | HTTPS FTP |
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-Related structure data
Related structure data | 3iv9C 3bulS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 65175.504 Da / Num. of mol.: 1 Fragment: C-terminal activation complex (UNP residues 649-1227) Mutation: I690C, G743C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b4019, JW3979, metH / Plasmid: PVB8 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: P13009, methionine synthase | ||
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#2: Chemical | ChemComp-B12 / | ||
#3: Chemical | ChemComp-SAH / | ||
#4: Chemical | ChemComp-NO3 / #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: 3.11 Å3/Da / Density % sol: 60.4 % |
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Crystal grow | Temperature: 302 K / Method: vapor diffusion / pH: 7 Details: 0.2 M potassium nitrate, 18 % (w/v) PEG3350, pH 7.0, VAPOR DIFFUSION, temperature 302K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9793 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 2, 2007 Details: K-B pair of biomorph mirrors for vertical and horizontal focusing |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 23160 / Num. obs: 23160 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.4 % / Rmerge(I) obs: 0.043 / Rsym value: 0.085 / Net I/σ(I): 27.3 |
Reflection shell | Resolution: 2.7→2.86 Å / Redundancy: 22.4 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 5.82 / Rsym value: 0.622 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Individual domains of PDB entry 3BUL Resolution: 2.7→45.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3333675.2 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.9901 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 76.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→45.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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