+Open data
-Basic information
Entry | Database: PDB / ID: 1k7y | ||||||
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Title | E. coli MetH C-terminal fragment (649-1227) | ||||||
Components | methionine synthase | ||||||
Keywords | TRANSFERASE / MOTION OF 4-HELIX BUNDLE / DOMAIN INTERACTIONS | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Bandarian, V. / Pattridge, K.A. / Lennon, B.W. / Huddler, D.P. / Matthews, R.G. / Ludwig, M.L. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2002 Title: Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. Authors: Bandarian, V. / Pattridge, K.A. / Lennon, B.W. / Huddler, D.P. / Matthews, R.G. / 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 | 1k7y.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k7y.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 1k7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k7y_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 1k7y_full_validation.pdf.gz | 507.2 KB | Display | |
Data in XML | 1k7y_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 1k7y_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/1k7y ftp://data.pdbj.org/pub/pdb/validation_reports/k7/1k7y | HTTPS FTP |
-Related structure data
Related structure data | 1k98C 1bmtS 1mskS 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: 64859.137 Da / Num. of mol.: 1 / Fragment: c-terminal activation complex, residues 651-1227 / Mutation: H759G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Escherichia coli / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue / References: UniProt: P13009, methionine synthase | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-B12 / | #4: 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: 3.45 Å3/Da / Density % sol: 64.31 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: cacodylate, ammonium sulfate, PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 17, 2000 / Details: Yale mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 18414 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Rsym value: 0.08 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.396 / % possible all: 95.4 |
Reflection | *PLUS Lowest resolution: 27 Å / Num. obs: 18245 / Num. measured all: 80208 / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 95.4 % / Rmerge(I) obs: 0.396 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entries 1msk and 1bmt Resolution: 3→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→15 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 15 Å / σ(F): 0 / Rfactor obs: 0.218 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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