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Yorodumi- PDB-6fbp: Human Methionine Adenosyltransferase II mutant (S114A) in P22121 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fbp | ||||||
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Title | Human Methionine Adenosyltransferase II mutant (S114A) in P22121 crystal form | ||||||
Components | S-adenosylmethionine synthase isoform type-2 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / cellular response to methionine / Methylation / S-adenosylmethionine biosynthetic process / protein heterooligomerization / protein hexamerization / small molecule binding / positive regulation of TORC1 signaling ...methionine adenosyltransferase complex / methionine adenosyltransferase / methionine adenosyltransferase activity / cellular response to methionine / Methylation / S-adenosylmethionine biosynthetic process / protein heterooligomerization / protein hexamerization / small molecule binding / positive regulation of TORC1 signaling / 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: 1.65 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 | 6fbp.cif.gz | 174.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fbp.ent.gz | 134.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fbp_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 6fbp_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 6fbp_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 6fbp_validation.cif.gz | 49.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fb/6fbp ftp://data.pdbj.org/pub/pdb/validation_reports/fb/6fbp | HTTPS FTP |
-Related structure data
Related structure data | 6fbnC 6fboC 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 43704.625 Da / Num. of mol.: 2 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 , 8 types, 500 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-PPK / ( | #8: Chemical | ChemComp-ADN / | #9: 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: 2.08 Å3/Da / Density % sol: 40.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% PEG600 0.1M HEPES |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→54.08 Å / Num. obs: 81704 / % possible obs: 97.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.068 / Rrim(I) all: 0.128 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4041 / CC1/2: 0.685 / Rpim(I) all: 0.372 / Rrim(I) all: 0.681 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5a1i Resolution: 1.65→54.08 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.421 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / 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: 19.747 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→54.08 Å
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