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Yorodumi- PDB-7p8m: Crystal structure of L147A/I351A variant of S-adenosylmethionine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p8m | ||||||
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Title | Crystal structure of L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii in complex with DMNB-SAM (4,5-dimethoxy-2-nitro benzyme S-adenosyl-methionine) | ||||||
Components | S-adenosylmethionine synthase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Herrmann, E. / Peters, A. / Cornelissen, N.V. / Rentmeister, A. / Kuemmel, D. | ||||||
Citation | Journal: Chembiochem / Year: 2022 Title: Visible-Light Removable Photocaging Groups Accepted by MjMAT Variant: Structural Basis and Compatibility with DNA and RNA Methyltransferases. Authors: Peters, A. / Herrmann, E. / Cornelissen, N.V. / Klocker, N. / Kummel, D. / Rentmeister, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p8m.cif.gz | 320.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p8m.ent.gz | 260 KB | Display | PDB format |
PDBx/mmJSON format | 7p8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p8m_validation.pdf.gz | 861.8 KB | Display | wwPDB validaton report |
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Full document | 7p8m_full_validation.pdf.gz | 866.7 KB | Display | |
Data in XML | 7p8m_validation.xml.gz | 33 KB | Display | |
Data in CIF | 7p8m_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/7p8m ftp://data.pdbj.org/pub/pdb/validation_reports/p8/7p8m | HTTPS FTP |
-Related structure data
Related structure data | 7p82SC 7p83C 7p84C 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: 47401.336 Da / Num. of mol.: 2 / Mutation: L147A/I351A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: mat, MJ1208 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58605, methionine adenosyltransferase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-6IH / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.62 Å3/Da / Density % sol: 53.06 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 0.1 M sodium acetate pH 4.6, 40% (v/v) PEG200 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→48.19 Å / Num. obs: 198161 / % possible obs: 99.8 % / Redundancy: 10.32 % / Biso Wilson estimate: 27.03 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.15 / Net I/σ(I): 10.59 |
Reflection shell | Resolution: 1.71→1.81 Å / Redundancy: 9.69 % / Mean I/σ(I) obs: 0.72 / Num. unique obs: 31710 / CC1/2: 0.54 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7P82 Resolution: 1.71→42.854 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.14 Å2 / Biso mean: 36.42 Å2 / Biso min: 15.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.71→42.854 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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