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Yorodumi- PDB-5evj: X-ray crystal structure of CrArsM, an arsenic (III) S-adenosylmet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5evj | ||||||
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Title | X-ray crystal structure of CrArsM, an arsenic (III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii | ||||||
Components | Arsenite methyltransferase | ||||||
Keywords | TRANSFERASE / METHYLTRANSFERASE / Arsenic Methyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Chlamydomonas reinhardtii (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Packianathan, C. / Kandavelu, P. / Sankaran, B. / Rosen, B.P. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal structure of CrArsM, an arsenic (III) S-adenosylmethionine methyltransferase from Chlamydomonas reinhardtii Authors: Packianathan, C. / Kandavelu, P. / 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 | 5evj.cif.gz | 137.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5evj.ent.gz | 105.3 KB | Display | PDB format |
PDBx/mmJSON format | 5evj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/5evj ftp://data.pdbj.org/pub/pdb/validation_reports/ev/5evj | HTTPS FTP |
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-Related structure data
Related structure data | 4fs8S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41621.465 Da / Num. of mol.: 2 Mutation: Y72W, C92A, C98A, C132A, C185A, C234A, C247A, C284A, C321A, W332Y, C352A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: arsM / Plasmid: PET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K0BVM7 #2: Chemical | ChemComp-NA / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 10% PEG 8000, 2.0 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. all: 34690 / Num. obs: 34690 / % possible obs: 100 % / Redundancy: 11.7 % / Biso Wilson estimate: 45.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 6.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FS8 Resolution: 2.4→45.58 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.341 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 43.03 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→45.58 Å
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