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Yorodumi- PDB-7n7i: X-ray crystal structure of Viperin-like enzyme from Trichoderma virens -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n7i | ||||||||||||||||||
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Title | X-ray crystal structure of Viperin-like enzyme from Trichoderma virens | ||||||||||||||||||
Components | Viperin-like enzyme | ||||||||||||||||||
Keywords | ANTIVIRAL PROTEIN / radical SAM protein / metalloprotein / antiviral / ddh-synthase | ||||||||||||||||||
Function / homology | Function and homology information iron-sulfur cluster binding / catalytic activity / mitochondrion / metal ion binding Similarity search - Function | ||||||||||||||||||
Biological species | Hypocrea virens (fungus) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å | ||||||||||||||||||
Authors | Grove, T.L. / Almo, S.C. / Bonanno, J.B. / Lachowicz, J.C. / Gizzi, A.G. | ||||||||||||||||||
Funding support | United States, 5items
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Citation | Journal: Biochemistry / Year: 2021 Title: Structural Insight into the Substrate Scope of Viperin and Viperin-like Enzymes from Three Domains of Life. Authors: Lachowicz, J.C. / Gizzi, A.S. / Almo, S.C. / Grove, T.L. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7n7i.cif.gz | 186.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n7i.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 7n7i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n7/7n7i ftp://data.pdbj.org/pub/pdb/validation_reports/n7/7n7i | HTTPS FTP |
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-Related structure data
Related structure data | 7n7hC 5vslS 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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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: 18 - 298 / Label seq-ID: 40 - 320
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-Components
#1: Protein | Mass: 37797.598 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hypocrea virens (strain Gv29-8 / FGSC 10586) (fungus) Strain: Gv29-8 / FGSC 10586 / Gene: TRIVIDRAFT_58105 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G9MQB8 #2: Chemical | #3: Chemical | #4: Chemical | 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: 2.1 Å3/Da / Density % sol: 41.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris-HCl, pH 8.5, 0.2 M sodium chloride, 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9893 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2017 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9893 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 3.19→28.14 Å / Num. obs: 15361 / % possible obs: 98.8 % / Redundancy: 10.3 % / CC1/2: 0.982 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.129 / Rrim(I) all: 0.409 / Net I/σ(I): 8.46 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VSL Resolution: 3.19→28.14 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0.11 / Phase error: 26.25 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.75 Å2 / Biso mean: 42.9874 Å2 / Biso min: 13.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.19→28.14 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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