+Open data
-Basic information
Entry | Database: PDB / ID: 6fbn | ||||||
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Title | Human Methionine Adenosyltransferase II mutant (Q113A) | ||||||
Components | S-adenosylmethionine synthase isoform type-2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / Methylation / S-adenosylmethionine biosynthetic process / 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 / Methylation / S-adenosylmethionine biosynthetic process / 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 / Resolution: 2.7 Å | ||||||
Authors | Panmanee, J. / Antonyuk, S.V. / Hasnain, S.S. | ||||||
Citation | Journal: Febs J. / Year: 2019 Title: Control and regulation of S-Adenosylmethionine biosynthesis by the regulatory beta subunit and quinolone-based compounds. Authors: Panmanee, J. / Bradley-Clarke, J. / Mato, J.M. / O'Neill, P.M. / 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 | 6fbn.cif.gz | 160.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fbn.ent.gz | 123.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fbn_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 6fbn_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6fbn_validation.xml.gz | 28 KB | Display | |
Data in CIF | 6fbn_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fbn ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fbn | HTTPS FTP |
-Related structure data
Related structure data | 6fboC 6fbpC 6fcbC 6fcdC 6g6rC 5a1iS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43663.570 Da / Num. of mol.: 2 / Mutation: Q113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAT2A, AMS2, MATA2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P31153, methionine adenosyltransferase |
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-Non-polymers , 7 types, 97 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-SAM / | #5: Chemical | ChemComp-PPK / ( | #6: Chemical | #7: Chemical | ChemComp-K / | #8: 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: 2.22 Å3/Da / Density % sol: 44.64 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% PEG600 0.1M HEPES pH7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9282 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→103.93 Å / Num. obs: 20580 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 44.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.096 / Rrim(I) all: 0.173 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.7→2.83 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.776 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2705 / CC1/2: 0.698 / Rpim(I) all: 0.942 / Rrim(I) all: 0.937 / Χ2: 43.844 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A1I Resolution: 2.7→103.93 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.684 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R Free: 0.286 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.82 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→103.93 Å
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Refine LS restraints |
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