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Yorodumi- PDB-6sw6: Crystal structure R264H mutant of the human S-adenosylmethionine ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sw6 | ||||||
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Title | Crystal structure R264H mutant of the human S-adenosylmethionine synthetase 1 | ||||||
Components | S-adenosylmethionine synthase isoform type-1 | ||||||
Keywords | TRANSFERASE / S-adenosylmethionine synthesis | ||||||
Function / homology | Function and homology information Defective MAT1A causes MATD / methionine catabolic process / Sulfur amino acid metabolism / methionine adenosyltransferase complex / Metabolism of ingested SeMet, Sec, MeSec into H2Se / methionine adenosyltransferase / methionine adenosyltransferase activity / Methylation / S-adenosylmethionine biosynthetic process / one-carbon metabolic process ...Defective MAT1A causes MATD / methionine catabolic process / Sulfur amino acid metabolism / methionine adenosyltransferase complex / Metabolism of ingested SeMet, Sec, MeSec into H2Se / methionine adenosyltransferase / methionine adenosyltransferase activity / Methylation / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / protein homotetramerization / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Panmanee, J. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Structural basis of the dominant inheritance of hypermethioninemia associated with the Arg264His mutation in the MAT1A gene. Authors: Panmanee, J. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sw6.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sw6.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 6sw6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6sw6_validation.pdf.gz | 436.7 KB | Display | wwPDB validaton report |
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Full document | 6sw6_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 6sw6_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 6sw6_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6sw6 ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6sw6 | HTTPS FTP |
-Related structure data
Related structure data | 6sw5C 2obvS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: 16 - 395 / Label seq-ID: 16 - 395
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-Components
#1: Protein | Mass: 43684.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver / Cell: Hepatocyte / Gene: MAT1A, AMS1, MATA1 / Organ: Liver / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q00266, methionine adenosyltransferase #2: Water | ChemComp-HOH / | |
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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: 2.3 Å3/Da / Density % sol: 46.62 % / Description: Pyramidal crystals |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 200 mM NaF, 20 % PEG 3350 and 15 % ethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→51.87 Å / Num. obs: 17484 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 55.573 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.092 / Rrim(I) all: 0.211 / Net I/σ(I): 5.1 |
Reflection shell | Resolution: 2.85→3 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2499 / CC1/2: 0.755 / Rpim(I) all: 0.447 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OBV Resolution: 2.85→51.87 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.865 / SU B: 23.967 / SU ML: 0.451 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.491 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.14 Å2 / Biso mean: 59.422 Å2 / Biso min: 31.44 Å2
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Refinement step | Cycle: final / Resolution: 2.85→51.87 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 22022 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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