+Open data
-Basic information
Entry | Database: PDB / ID: 6l25 | |||||||||||||||
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Title | Deoxyribonuclease from Staphylococcus aureus | |||||||||||||||
Components | Deoxyribonuclease YcfH | |||||||||||||||
Keywords | METAL BINDING PROTEIN / DNA binding protein / DNase / RNase / DNA repair system. | |||||||||||||||
Function / homology | Function and homology information endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / exonuclease activity Similarity search - Function | |||||||||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å | |||||||||||||||
Authors | Lee, K.-Y. / Kim, D.-G. / Lee, B.-J. | |||||||||||||||
Funding support | Korea, Republic Of, 4items
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Citation | Journal: Iucrj / Year: 2020 Title: A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease. Authors: Lee, K.-Y. / Cheon, S.-H. / Kim, D.-G. / Lee, S.J. / Lee, B.-J. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6l25.cif.gz | 116.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6l25.ent.gz | 93.5 KB | Display | PDB format |
PDBx/mmJSON format | 6l25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l2/6l25 ftp://data.pdbj.org/pub/pdb/validation_reports/l2/6l25 | HTTPS FTP |
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-Related structure data
Similar structure data |
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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: 31410.607 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: yabD, tatP, ycfH, ycfH_1, BN1321_120011, C7P97_09010, CSC83_12190, CSC87_02770, EP54_03105, EQ90_10980, ERS072840_02446, HMPREF3211_00370, M1K003_2676, NCTC10654_00570, NCTC10702_00886, ...Gene: yabD, tatP, ycfH, ycfH_1, BN1321_120011, C7P97_09010, CSC83_12190, CSC87_02770, EP54_03105, EQ90_10980, ERS072840_02446, HMPREF3211_00370, M1K003_2676, NCTC10654_00570, NCTC10702_00886, NCTC13131_01111, NCTC5664_00191, NCTC7878_00052, RK64_02970, SAMEA1708674_03251 Production host: Escherichia coli K-12 (bacteria) References: UniProt: W8U6D8, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters #2: Chemical | ChemComp-NI / #3: Chemical | ChemComp-PO4 / #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: 2.34 Å3/Da / Density % sol: 47.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4 M sodium malonate, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 47022 / % possible obs: 98.6 % / Redundancy: 9.6 % / CC1/2: 0.989 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 7.8 % / Num. unique obs: 2125 / CC1/2: 0.872 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.007 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.61 Å2 / Biso mean: 25.49 Å2 / Biso min: 12.7 Å2
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Refinement step | Cycle: final / Resolution: 1.85→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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