+Open data
-Basic information
Entry | Database: PDB / ID: 8kbi | ||||||
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Title | Structure of apo-AcrIIA7 | ||||||
Components | Inhibitor of Type II CRISPR-Cas system | ||||||
Keywords | VIRAL PROTEIN / AcrIIA7 | ||||||
Function / homology | Protein of unknown function DUF2829 / Protein of unknown function (DUF2829) / Inhibitor of Type II CRISPR-Cas system Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Xiao, Y. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of apo-AcrIIA7 Authors: Xiao, Y. / Feng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kbi.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kbi.ent.gz | 80.7 KB | Display | PDB format |
PDBx/mmJSON format | 8kbi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kbi_validation.pdf.gz | 449.2 KB | Display | wwPDB validaton report |
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Full document | 8kbi_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 8kbi_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 8kbi_validation.cif.gz | 31.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/8kbi ftp://data.pdbj.org/pub/pdb/validation_reports/kb/8kbi | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 12016.822 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) metagenome (others) / Gene: acrIIA7 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A447EB45 #2: 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: 50.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.0 M Lithium chloride, 20% w/v Polyethylene glycol 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.71 Å / Num. obs: 101128 / % possible obs: 100 % / Redundancy: 39.9 % / Rrim(I) all: 0.28 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 40 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 5207 / Rrim(I) all: 1.886 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→19.71 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 27.77 / 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: 1.7→19.71 Å
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Refine LS restraints |
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LS refinement shell |
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