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Yorodumi- PDB-4fr0: ArsM arsenic(III) S-adenosylmethionine methyltransferase with SAM -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fr0 | |||||||||
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Title | ArsM arsenic(III) S-adenosylmethionine methyltransferase with SAM | |||||||||
Components | Arsenic methyltransferase | |||||||||
Keywords | TRANSFERASE / Rossmann Fold / Arsenic Methyltransferase | |||||||||
Function / homology | Function and homology information arsenite methyltransferase activity / arsonoacetate metabolic process / : / toxin metabolic process / methylation / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Cyanidioschyzon sp. 5508 (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | |||||||||
Authors | Ajees, A.A. / Marapakala, K. / Packianathan, C. / Sankaran, B. / Rosen, B.P. | |||||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Structure of an As(III) S-Adenosylmethionine Methyltransferase: Insights into the Mechanism of Arsenic Biotransformation. Authors: Ajees, A.A. / Marapakala, K. / Packianathan, C. / Sankaran, B. / Rosen, B.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fr0.cif.gz | 79.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fr0.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fr0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fr0_validation.pdf.gz | 708.1 KB | Display | wwPDB validaton report |
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Full document | 4fr0_full_validation.pdf.gz | 714.3 KB | Display | |
Data in XML | 4fr0_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 4fr0_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/4fr0 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/4fr0 | HTTPS FTP |
-Related structure data
Related structure data | 4fs8SC 4fsdC 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
#1: Protein | Mass: 42312.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanidioschyzon sp. 5508 (eukaryote) / Strain: 5508 / Gene: arsM / Plasmid: pET28(+) / Production host: Escherichia coli (E. coli) / References: UniProt: C0JV69 |
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#2: Chemical | ChemComp-SAM / |
Nonpolymer details | AUTHOR STATES THAT THE ELECTRON DENSITY FOR THE METHIONINE MOIETY OF THE SAM LIGAND, WHICH INCLUDES ...AUTHOR STATES THAT THE ELECTRON DENSITY FOR THE METHIONINE |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.72 % |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 4.2 Details: 20% PEG 8000, 0.2 M NaCl, 0.1 M Citrate Phosphate, 10 mM TCEP, pH 4.2, EVAPORATION, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 4, 2010 / Details: mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→50 Å / Num. obs: 11298 / % possible obs: 99.98 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 63.3 Å2 / Rmerge(I) obs: 0.098 |
Reflection shell | Resolution: 2.75→2.87 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1394 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FS8 Resolution: 2.75→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 13.849 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R: 1.531 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.264 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→50 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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