+Open data
-Basic information
Entry | Database: PDB / ID: 8kbk | ||||||
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Title | Structure of AcrIIA7 complexed with 1',2'-cADPR and cGG | ||||||
Components | Inhibitor of Type II CRISPR-Cas system | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Protein of unknown function DUF2829 / Protein of unknown function (DUF2829) / Chem-C2E / Chem-MF6 / Inhibitor of Type II CRISPR-Cas system Function and homology information | ||||||
Biological species | metagenome (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Xiao, Y. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of AcrIIA7 complexed with 1',2'-cADPR and cGG 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 | 8kbk.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kbk.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 8kbk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kbk_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 8kbk_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 8kbk_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8kbk_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/8kbk ftp://data.pdbj.org/pub/pdb/validation_reports/kb/8kbk | 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
#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: Chemical | #3: Chemical | #4: 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: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Potassium thiocyanate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 15, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→47.76 Å / Num. obs: 21073 / % possible obs: 98.2 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.101 / Χ2: 1 / Net I/σ(I): 11.5 / Num. measured all: 143086 |
Reflection shell | Resolution: 2.28→2.34 Å / % possible obs: 97.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.211 / Num. measured all: 9675 / Num. unique obs: 1528 / CC1/2: 0.73 / Rpim(I) all: 0.523 / Rrim(I) all: 1.322 / Χ2: 0.96 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.28→27.08 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→27.08 Å
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Refine LS restraints |
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LS refinement shell |
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