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Yorodumi- PDB-4rsr: ArsM arsenic(III) S-adenosylmethionine methyltransferase with tri... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rsr | |||||||||
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Title | ArsM arsenic(III) S-adenosylmethionine methyltransferase with trivalent phenyl arsencial derivative-Roxarsone | |||||||||
Components | Arsenic methyltransferase | |||||||||
Keywords | TRANSFERASE / Rossman 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. (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | |||||||||
Authors | Packianathan, C. / Marapakala, K. / Ajees, A.A. / Kandavelu, P. / Rosen, B.P. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2015 Title: A disulfide-bond cascade mechanism for arsenic(III) S-adenosylmethionine methyltransferase. Authors: Marapakala, K. / Packianathan, C. / Ajees, A.A. / Dheeman, D.S. / Sankaran, B. / Kandavelu, P. / 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 | 4rsr.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rsr.ent.gz | 61.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rsr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rsr_validation.pdf.gz | 464.1 KB | Display | wwPDB validaton report |
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Full document | 4rsr_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 4rsr_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 4rsr_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/4rsr ftp://data.pdbj.org/pub/pdb/validation_reports/rs/4rsr | HTTPS FTP |
-Related structure data
Related structure data | 4kw7C 4fs8S 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, 1 molecules A
#1: Protein | Mass: 42312.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanidioschyzon sp. (eukaryote) / Strain: 5508 / Gene: arsM / Plasmid: PET28(a) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C0JV69 |
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-Non-polymers , 6 types, 130 molecules
#2: Chemical | ChemComp-RXO / | ||||||
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#3: Chemical | ChemComp-MG / | ||||||
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | ChemComp-DTT / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 18% polyethylene glycol3000, 0.2 M calcium acetate and 0.1 M Tris-HCl pH 7.0, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 31, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. all: 120150 / Num. obs: 16680 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 6.2 / Num. unique all: 762 / Rsym value: 0.25 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4FS8 Resolution: 2.25→39.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.006 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.308 / ESU R Free: 0.218 / 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: 32.433 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→39.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.249→2.308 Å / Total num. of bins used: 20
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