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Yorodumi- PDB-6u1r: SxtG an amidinotransferase from the Microseira wollei in Saxitoxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6u1r | ||||||
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Title | SxtG an amidinotransferase from the Microseira wollei in Saxitoxin biosynthetic pathway | ||||||
Components | SxtG | ||||||
Keywords | TRANSFERASE / amidinotransferase / saxitoxin biosynthetic pathway / SxtG | ||||||
Function / homology | amidinotransferase activity / Glycine/inosamine-phosphate amidinotransferase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta / FORMIC ACID / SxtG Function and homology information | ||||||
Biological species | Microseira wollei (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.792 Å | ||||||
Authors | Mallik, L. / Lukowski, A.L. / Narayan, A.R.H. / Koutmos, M. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Substrate Promiscuity of a Paralytic Shellfish Toxin Amidinotransferase. Authors: Lukowski, A.L. / Mallik, L. / Hinze, M.E. / Carlson, B.M. / Ellinwood, D.C. / Pyser, J.B. / Koutmos, M. / Narayan, A.R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6u1r.cif.gz | 284.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6u1r.ent.gz | 230.9 KB | Display | PDB format |
PDBx/mmJSON format | 6u1r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u1r_validation.pdf.gz | 444.4 KB | Display | wwPDB validaton report |
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Full document | 6u1r_full_validation.pdf.gz | 449 KB | Display | |
Data in XML | 6u1r_validation.xml.gz | 31 KB | Display | |
Data in CIF | 6u1r_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/6u1r ftp://data.pdbj.org/pub/pdb/validation_reports/u1/6u1r | HTTPS FTP |
-Related structure data
Related structure data | 1jdwS S: Starting model for refinement |
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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: 43887.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Microseira wollei (bacteria) / Gene: sxtG / Plasmid: pET151 / Details (production host): T7 promoter and TEV cleavable / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LEMO21 / References: UniProt: C3RVP0 #2: Chemical | ChemComp-FMT / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.47 Å3/Da / Density % sol: 50.21 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG 3350, 0.2 M ammonium acetate and 0.1 M bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 13, 2018 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→48.1 Å / Num. obs: 77125 / % possible obs: 99.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 29.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.091 / Χ2: 0.087 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.79→1.83 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4162 / CC1/2: 0.871 / Rpim(I) all: 0.282 / Rrim(I) all: 0.733 / Χ2: 0.76 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JDW Resolution: 1.792→48.071 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.792→48.071 Å
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Refine LS restraints |
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LS refinement shell |
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