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Yorodumi- PDB-8izt: Crystal structure of the N-terminal domain (residues 1-121) of MPXV A7 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8izt | ||||||
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Title | Crystal structure of the N-terminal domain (residues 1-121) of MPXV A7 | ||||||
Components | Virion morphogenesis protein OPG132 | ||||||
Keywords | VIRAL PROTEIN / MPXV / A7 / N-terminus | ||||||
Function / homology | Poxvirus A6 / Poxvirus A6 protein / virion component / host cell cytoplasm / Virion morphogenesis protein OPG132 Function and homology information | ||||||
Biological species | Monkeypox virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Ni, X.C. / Lei, J. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Crystal structure of the N-terminal domain (residues 1-121) of MPXV A7 Authors: Ni, X.C. / Lei, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8izt.cif.gz | 44 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8izt.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 8izt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/8izt ftp://data.pdbj.org/pub/pdb/validation_reports/iz/8izt | HTTPS FTP |
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-Related structure data
Related structure data | 6cb6S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 14280.537 Da / Num. of mol.: 1 / Fragment: N-terminal domain (residues 1-121) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Monkeypox virus / Gene: OPG132, MPXVgp117 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7H0DNA4 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.91 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0,01 M Zinc chloride, 0.1 M MES pH 6.0, 20% w/v PEG6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→35.1 Å / Num. obs: 10782 / % possible obs: 99.7 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.74→1.77 Å / Num. unique obs: 612 / CC1/2: 0.255 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CB6 Resolution: 1.74→35.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.553 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.124 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.466 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→35.1 Å
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Refine LS restraints |
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LS refinement shell |
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