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- PDB-7p82: Crystal structure of apo form L147A/I351A variant of S-adenosylme... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7p82 | ||||||
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Title | Crystal structure of apo form L147A/I351A variant of S-adenosylmethionine synthetase from Methanocaldococcus jannaschii | ||||||
![]() | S-adenosylmethionine synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Herrmann, E. / Peters, A. / Cornelissen, N.V. / Rentmeister, A. / Kuemmel, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 314.8 KB | Display | ![]() |
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PDB format | ![]() | 257.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442 KB | Display | ![]() |
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Full document | ![]() | 446.2 KB | Display | |
Data in XML | ![]() | 32.1 KB | Display | |
Data in CIF | ![]() | 46.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7p83C ![]() 7p84C ![]() 7p8mC ![]() 4l7iS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: mat, MJ1208 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.12 % |
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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: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 3, 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: 2.04→47.96 Å / Num. obs: 59592 / % possible obs: 98.3 % / Redundancy: 16.07 % / CC1/2: 0.997 / Rrim(I) all: 0.165 / Net I/σ(I): 10.99 |
Reflection shell | Resolution: 2.04→2.17 Å / Redundancy: 11.77 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 8708 / CC1/2: 0.882 / Rrim(I) all: 0.849 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4L7I Resolution: 2.042→47.958 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.75 / 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: 154.52 Å2 / Biso mean: 43.53 Å2 / Biso min: 19.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.042→47.958 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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