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Yorodumi- PDB-6wk3: Engineered carbene transferase RmaNOD Q52V, putative nitric oxide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wk3 | ||||||||||||||||||
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Title | Engineered carbene transferase RmaNOD Q52V, putative nitric oxide dioxygenase from Rhodothermus marinus | ||||||||||||||||||
Components | Nitric oxide dioxygenase | ||||||||||||||||||
Keywords | METAL BINDING PROTEIN / Heme binding protein / Carbene transferase / Globin | ||||||||||||||||||
Function / homology | Function and homology information nitric oxide dioxygenase / nitric oxide dioxygenase NAD(P)H activity / response to nitrosative stress / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Rhodothermus marinus DSM 4252 (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | ||||||||||||||||||
Authors | Knight, A.M. / Arnold, F.H. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Acs Catalysis / Year: 2020 Title: Diversity-Oriented Enzymatic Synthesis of Cyclopropane Building Blocks. Authors: Wittmann, B.J. / Knight, A.M. / Hofstra, J.L. / Reisman, S.E. / Kan, S.B.J. / Arnold, F.H. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wk3.cif.gz | 287.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wk3.ent.gz | 194.4 KB | Display | PDB format |
PDBx/mmJSON format | 6wk3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wk3_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6wk3_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6wk3_validation.xml.gz | 23 KB | Display | |
Data in CIF | 6wk3_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wk/6wk3 ftp://data.pdbj.org/pub/pdb/validation_reports/wk/6wk3 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16391.928 Da / Num. of mol.: 4 / Mutation: Q52V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodothermus marinus DSM 4252 (bacteria) Strain: ATCC 43812 / DSM 4252 / R-10 / Gene: Rmar_2776 / Plasmid: pSUMO_RmaNOD_Q52V Details (production host): pET22b encoding RmaNOD Q52V with N-terminal His-SUMO tag Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0MGT2, nitric oxide dioxygenase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-CU / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 4.07 Å3/Da / Density % sol: 69.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 40 mM Cu(II)SO4, 0.1M HEPES pH 7.6, 1.2 M sodium acetate trihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.74035 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.74035 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→43.65 Å / Num. obs: 36944 / % possible obs: 95.98 % / Redundancy: 6.7 % / Biso Wilson estimate: 58.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.064 / Rrim(I) all: 0.123 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.45→2.538 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 3602 / CC1/2: 0.717 / Rpim(I) all: 0.79 / Rrim(I) all: 1.462 / % possible all: 94.17 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→41.67 Å / SU ML: 0.3288 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.3732 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→41.67 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.07758944232 Å / Origin y: 16.3263764547 Å / Origin z: 33.3602071872 Å
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Refinement TLS group | Selection details: all |