+Open data
-Basic information
Entry | Database: PDB / ID: 6uxf | ||||||
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Title | Structure of V. metoecus NucC, hexamer form | ||||||
Components | Vibrio meotecus sp. RC341 NucC | ||||||
Keywords | DNA BINDING PROTEIN / Nuclease | ||||||
Function / homology | Domain of unknown function DUF6602 / Domain of unknown function (DUF6602) / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / nucleotide binding / metal ion binding / CRISPR-associated endodeoxyribonuclease NucC Function and homology information | ||||||
Biological species | Vibrio metoecus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Ye, Q. / Corbett, K.D. | ||||||
Citation | Journal: Mol.Cell / Year: 2020 Title: Structure and Mechanism of a Cyclic Trinucleotide-Activated Bacterial Endonuclease Mediating Bacteriophage Immunity. Authors: Lau, R.K. / Ye, Q. / Birkholz, E.A. / Berg, K.R. / Patel, L. / Mathews, I.T. / Watrous, J.D. / Ego, K. / Whiteley, A.T. / Lowey, B. / Mekalanos, J.J. / Kranzusch, P.J. / Jain, M. / Pogliano, J. / Corbett, K.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uxf.cif.gz | 189.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uxf.ent.gz | 126.7 KB | Display | PDB format |
PDBx/mmJSON format | 6uxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uxf_validation.pdf.gz | 246.7 KB | Display | wwPDB validaton report |
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Full document | 6uxf_full_validation.pdf.gz | 246.7 KB | Display | |
Data in XML | 6uxf_validation.xml.gz | 1 KB | Display | |
Data in CIF | 6uxf_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ux/6uxf ftp://data.pdbj.org/pub/pdb/validation_reports/ux/6uxf | HTTPS FTP |
-Related structure data
Related structure data | 6p7oSC 6p7pC 6p7qC 6q1hC 6uxgC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data set type: diffraction image data / Details: raw diffraction data / Metadata reference: 10.15785/SBGRID/735 |
-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: 28072.033 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio metoecus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0DUD6*PLUS |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 0.1 M sodium formate, 14% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→100 Å / Num. obs: 55873 / % possible obs: 98.5 % / Redundancy: 33.5 % / Biso Wilson estimate: 28.28 Å2 / CC1/2: 1 / Rrim(I) all: 0.066 / Rsym value: 0.065 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.65→1.75 Å / Mean I/σ(I) obs: 1.85 / Num. unique obs: 8767 / CC1/2: 0.669 / Rrim(I) all: 1.57 / Rsym value: 1.527 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6P7O Resolution: 1.65→69.2 Å / SU ML: 0.1941 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.8837
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.45 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→69.2 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 46.9509903729 Å / Origin y: -42.2455099475 Å / Origin z: -3.81082839784 Å
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Refinement TLS group | Selection details: chain A |