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Yorodumi- PDB-7l1a: Human Methionine Adenosyltransferase 2A bound to Methylthioadenos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7l1a | |||||||||
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Title | Human Methionine Adenosyltransferase 2A bound to Methylthioadenosine and inhibitor, di-imido triphosphate (PNPNP) | |||||||||
Components | S-adenosylmethionine synthase isoform type-2 | |||||||||
Keywords | TRANSFERASE/INHIBITOR / S-adenosylmethionine / SAM synthetase / enzyme mechanism / inhibitor / TRANSFERASE-INHIBITOR complex | |||||||||
Function / homology | Function and homology information methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / Methylation / protein heterooligomerization / protein hexamerization / small molecule binding / cellular response to leukemia inhibitory factor / one-carbon metabolic process / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å | |||||||||
Authors | Niland, C.N. / Fedorov, E. / Schramm, V.L. / Ghosh, A. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Biochemistry / Year: 2021 Title: Mechanism and Inhibition of Human Methionine Adenosyltransferase 2A. Authors: Niland, C.N. / Ghosh, A. / Cahill, S.M. / Schramm, V.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7l1a.cif.gz | 253.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7l1a.ent.gz | 204.4 KB | Display | PDB format |
PDBx/mmJSON format | 7l1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l1/7l1a ftp://data.pdbj.org/pub/pdb/validation_reports/l1/7l1a | HTTPS FTP |
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-Related structure data
Related structure data | 5a1iS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46279.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31153, methionine adenosyltransferase |
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-Non-polymers , 7 types, 364 molecules
#2: Chemical | #3: Chemical | ChemComp-K / | #4: Chemical | ChemComp-XE1 / | #5: Chemical | ChemComp-MTA / | #6: Chemical | ChemComp-ALA / | #7: Chemical | ChemComp-NA / #8: Water | ChemComp-HOH / | |
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-Details
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: 2.03 Å3/Da / Density % sol: 39.43 % / Description: Plates |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: 0.2 M lithium citrate, 15% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2020 / Details: KB MIRRORS | ||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.25→18.92 Å / Num. obs: 103846 / % possible obs: 99.9 % / Redundancy: 12.3 % / Biso Wilson estimate: 7.55 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.05 / Rrim(I) all: 0.178 / Net I/σ(I): 12.2 / Num. measured all: 1272536 / Scaling rejects: 6302 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5A1I Resolution: 1.25→18.92 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12 / 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 mean: 11.76 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→18.92 Å
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LS refinement shell |
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