+Open data
-Basic information
Entry | Database: PDB / ID: 8kbb | ||||||
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Title | Structure of apo-CmTad1 | ||||||
Components | Thoeris anti-defense 1 | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | nucleotide binding / Thoeris anti-defense 1 Function and homology information | ||||||
Biological species | Clostridioides mangenotii LM2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å | ||||||
Authors | Xiao, Y. / Feng, Y. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of apo-CmTad1 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 | 8kbb.cif.gz | 327.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kbb.ent.gz | 267.5 KB | Display | PDB format |
PDBx/mmJSON format | 8kbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kbb_validation.pdf.gz | 530.7 KB | Display | wwPDB validaton report |
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Full document | 8kbb_full_validation.pdf.gz | 555 KB | Display | |
Data in XML | 8kbb_validation.xml.gz | 60.3 KB | Display | |
Data in CIF | 8kbb_validation.cif.gz | 83.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/8kbb ftp://data.pdbj.org/pub/pdb/validation_reports/kb/8kbb | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15194.333 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides mangenotii LM2 (bacteria) Strain: LM2 / Gene: tad1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW61 #2: Chemical | #3: 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: 4.19 Å3/Da / Density % sol: 70.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 2.0 M Ammonium sulfate, 1.4% v/v Polyethylene glycol 400 |
-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 X 9M / Detector: PIXEL / Date: Jun 17, 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: 2.56→42.28 Å / Num. obs: 97659 / % possible obs: 100 % / Redundancy: 12.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.069 / Rrim(I) all: 0.251 / Χ2: 0.93 / Net I/σ(I): 10.1 / Num. measured all: 1255851 |
Reflection shell | Resolution: 2.56→2.63 Å / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 2.489 / Num. measured all: 91653 / Num. unique obs: 7159 / CC1/2: 0.62 / Rpim(I) all: 0.719 / Rrim(I) all: 2.592 / Χ2: 0.8 / Net I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→41.13 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.13 / 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: 2.56→41.13 Å
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Refine LS restraints |
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LS refinement shell |
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