+Open data
-Basic information
Entry | Database: PDB / ID: 6maf | ||||||
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Title | native BbvCI A2B2 tetramer at low resolution | ||||||
Components |
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Keywords | HYDROLASE / endonuclease / DNA binding protein / Type IIT restriction enzyme | ||||||
Function / homology | Restriction endonuclease, type II, Bpu10I / Bpu10I restriction endonuclease / endonuclease activity / BbvCI endonuclease subunit 2 / BbvCI endonuclease subunit 1 Function and homology information | ||||||
Biological species | Brevibacillus brevis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.79 Å | ||||||
Authors | Shen, B.W. / Stoddard, B.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Authors: Shen, B.W. / Doyle, L. / Bradley, P. / Heiter, D.F. / Lunnen, K.D. / Wilson, G.G. / Stoddard, B.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6maf.cif.gz | 225.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6maf.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 6maf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6maf_validation.pdf.gz | 459.2 KB | Display | wwPDB validaton report |
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Full document | 6maf_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 6maf_validation.xml.gz | 40.5 KB | Display | |
Data in CIF | 6maf_validation.cif.gz | 53 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/6maf ftp://data.pdbj.org/pub/pdb/validation_reports/ma/6maf | HTTPS FTP |
-Related structure data
Related structure data | 6eg7SC 6m9gC 6magC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 31478.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: bbvCIR-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5D6Y5 #2: Protein | Mass: 32659.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brevibacillus brevis (bacteria) / Gene: bbvCIR-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5D6Y4 |
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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: 3.31 Å3/Da / Density % sol: 62.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 15% PEF4k, 0.2M Ammonium Sulfate, Citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 1, 2016 |
Radiation | Monochromator: yale mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.79→28.4 Å / Num. obs: 15368 / % possible obs: 98.9 % / Observed criterion σ(I): 1 / Redundancy: 5.1 % / Biso Wilson estimate: 137.6 Å2 / CC1/2: 0.784 / Rpim(I) all: 0.104 / Rrim(I) all: 0.1045 / Rsym value: 0.129 / Χ2: 1.009 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 3.792→3.889 Å / Redundancy: 5 % / Num. unique obs: 1117 / Rsym value: 1.47 / % possible all: 93.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EG7 Resolution: 3.79→28.4 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.82 / SU B: 73.611 / SU ML: 1.08 / Cross valid method: THROUGHOUT / ESU R Free: 1.125
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 177.963 Å2
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Refinement step | Cycle: 1 / Resolution: 3.79→28.4 Å
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Refine LS restraints |
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