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Yorodumi- PDB-7r2w: Mutant S-adenosylmethionine synthetase from E.coli complexed with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r2w | ||||||
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Title | Mutant S-adenosylmethionine synthetase from E.coli complexed with AMPPNP and methionine | ||||||
Components | S-adenosylmethionine synthase | ||||||
Keywords | TRANSFERASE / Dihedral D2 symmetry / homotetramer A4 symmetry / isologous interfaces 2 / S-adenosylmethionine synthetase | ||||||
Function / homology | Function and homology information methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Shahar, A. / Kleiner, D. / Bershtein, S. / Zarivach, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2022 Title: Evolution of homo-oligomerization of methionine S-adenosyltransferases is replete with structure-function constrains. Authors: Kleiner, D. / Shapiro Tuchman, Z. / Shmulevich, F. / Shahar, A. / Zarivach, R. / Kosloff, M. / Bershtein, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r2w.cif.gz | 164.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r2w.ent.gz | 127.1 KB | Display | PDB format |
PDBx/mmJSON format | 7r2w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r2w_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7r2w_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7r2w_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 7r2w_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/7r2w ftp://data.pdbj.org/pub/pdb/validation_reports/r2/7r2w | HTTPS FTP |
-Related structure data
Related structure data | 7r3bC 1p7lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 42826.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: metK / Production host: Escherichia coli (E. coli) / References: UniProt: C3SV92, methionine adenosyltransferase | ||||||
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#2: Chemical | ChemComp-ANP / | ||||||
#3: Chemical | #4: Chemical | ChemComp-K / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M L-Proline 0.1M Hepes pH 7.56 14% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97626 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 26, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→62.73 Å / Num. obs: 46194 / % possible obs: 99.96 % / Redundancy: 45.8 % / Biso Wilson estimate: 31.66 Å2 / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 26.2 |
Reflection shell | Resolution: 1.6→1.658 Å / Mean I/σ(I) obs: 0.4 / Num. unique obs: 4536 / CC1/2: 0.4 / Rrim(I) all: 4.035 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P7L Resolution: 1.6→62.73 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.327 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.14 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→62.73 Å
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Refine LS restraints |
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