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Yorodumi- PDB-7ccd: Sulfur binding domain of SprMcrA complexed with phosphorothioated DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ccd | ||||||||||||
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Title | Sulfur binding domain of SprMcrA complexed with phosphorothioated DNA | ||||||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / sulfur binding domain / restriction enzyme / phosphorothioated DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||
Function / homology | HNH endonuclease / HNH endonuclease / HNH nucleases / HNH nuclease / endonuclease activity / nucleic acid binding / zinc ion binding / DNA / Uncharacterized protein Function and homology information | ||||||||||||
Biological species | Streptomyces pristinaespiralis (bacteria) Escherichia coli B7A (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å | ||||||||||||
Authors | Yu, H. / Li, J. / Liu, G. / Zhao, G. / Wang, Y. / Hu, W. / Deng, Z. / Gan, J. / Zhao, Y. / He, X. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: DNA backbone interactions impact the sequence specificity of DNA sulfur-binding domains: revelations from structural analyses. Authors: Yu, H. / Li, J. / Liu, G. / Zhao, G. / Wang, Y. / Hu, W. / Deng, Z. / Wu, G. / Gan, J. / Zhao, Y.L. / He, X. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ccd.cif.gz | 188.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ccd.ent.gz | 146.1 KB | Display | PDB format |
PDBx/mmJSON format | 7ccd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/7ccd ftp://data.pdbj.org/pub/pdb/validation_reports/cc/7ccd | HTTPS FTP |
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-Related structure data
Related structure data | 7cc9C 7ccjC 5zmoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
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-Components
#1: Protein | Mass: 18848.174 Da / Num. of mol.: 2 / Fragment: Sulfur binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces pristinaespiralis (bacteria) Gene: SPRI_5136 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M4DML1 #2: DNA chain | Mass: 2980.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli B7A (bacteria) #3: DNA chain | Mass: 3126.106 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Escherichia coli B7A (bacteria) #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: 2.1 Å3/Da / Density % sol: 41.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: Ammonium acetate, BIS-TRIS pH5.5, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 30, 2016 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.42→28.63 Å / Num. obs: 13319 / % possible obs: 80.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 37.99 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.053 / Rrim(I) all: 0.101 / Net I/σ(I): 10.2 / Num. measured all: 46693 / Scaling rejects: 9 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ZMO Resolution: 2.42→28.626 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 26.32 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.33 Å2 / Biso mean: 47.7966 Å2 / Biso min: 21.89 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.42→28.626 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: -40.8177 Å / Origin y: -16.7683 Å / Origin z: -61.7455 Å
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Refinement TLS group |
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