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Yorodumi- PDB-5xto: Crystal structure of baculoviral sulfhydryl oxidase P33 (H114A mutant) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xto | ||||||
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Title | Crystal structure of baculoviral sulfhydryl oxidase P33 (H114A mutant) | ||||||
Components | FAD-linked sulfhydryl oxidase | ||||||
Keywords | OXIDOREDUCTASE / sulfhydryl oxidase | ||||||
Function / homology | FAD-linked sulfhydryl oxidase / Baculovirus P33 / thiol oxidase / thiol oxidase activity / host cell cytoplasm / host cell nucleus / FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase Function and homology information | ||||||
Biological species | Autographa californica nucleopolyhedrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Kuang, W. / Hu, Z. / Gong, P. | ||||||
Funding support | China, 1items
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Citation | Journal: J. Virol. / Year: 2017 Title: Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function Authors: Kuang, W. / Zhang, H. / Wang, M. / Zhou, N.Y. / Deng, F. / Wang, H. / Gong, P. / Hu, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xto.cif.gz | 214.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xto.ent.gz | 170.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xto_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 5xto_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 5xto_validation.xml.gz | 40.6 KB | Display | |
Data in CIF | 5xto_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/5xto ftp://data.pdbj.org/pub/pdb/validation_reports/xt/5xto | HTTPS FTP |
-Related structure data
Related structure data | 5xkiC 5xtnC 5xtpC 5xtqC 5xtrC 3qzyS 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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Unit cell |
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-Components
#1: Protein | Mass: 34459.871 Da / Num. of mol.: 4 / Mutation: H114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Autographa californica nucleopolyhedrovirus Gene: P33, ORF92 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41480, thiol oxidase #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
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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: 2.32 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.555→60 Å / Num. obs: 37851 / % possible obs: 93.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.16 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.98 / Net I/σ(I): 6.4 / Num. measured all: 142090 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.484 / Num. unique all: 4044 / CC1/2: 0.999 / Χ2: 0.992 / % possible all: 91.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QZY Resolution: 2.56→37.55 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.4
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.91 Å2 / Biso mean: 39.56 Å2 / Biso min: 17.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.56→37.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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