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Yorodumi- PDB-5zkm: Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zkm | ||||||||||||
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Title | Crystal structure of Streptococcus pneumoniae SP_0782 (residues 7-79) in complex with single-stranded DNA TCTTCC | ||||||||||||
Components |
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Keywords | UNKNOWN FUNCTION/DNA / protein-DNA complex / UNKNOWN FUNCTION-DNA complex | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Streptococcus pneumoniae TIGR4 (bacteria) synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||||||||
Authors | Lu, G. / Li, S. / Zhu, J. / Yang, Y. / Gong, P. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Structural insight into the length-dependent binding of ssDNA by SP_0782 from Streptococcus pneumoniae, reveals a divergence in the DNA-binding interface of PC4-like proteins. Authors: Li, S. / Lu, G. / Fang, X. / Ramelot, T.A. / Kennedy, M.A. / Zhou, X. / Gong, P. / Zhang, X. / Liu, M. / Zhu, J. / Yang, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zkm.cif.gz | 31.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zkm.ent.gz | 17.7 KB | Display | PDB format |
PDBx/mmJSON format | 5zkm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zkm_validation.pdf.gz | 421 KB | Display | wwPDB validaton report |
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Full document | 5zkm_full_validation.pdf.gz | 421 KB | Display | |
Data in XML | 5zkm_validation.xml.gz | 5.8 KB | Display | |
Data in CIF | 5zkm_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/5zkm ftp://data.pdbj.org/pub/pdb/validation_reports/zk/5zkm | HTTPS FTP |
-Related structure data
Related structure data | 5zklC 6jipC 6jiqC 3obhS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 9592.798 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Strain: ATCC BAA-334 / TIGR4 / Gene: SP_0782 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H2UPA7 |
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#2: DNA chain | Mass: 1735.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: 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: 2.1 Å3/Da / Density % sol: 41.32 % |
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Crystal grow | Temperature: 289 K / Method: evaporation / pH: 6.8 / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 5, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.65→50 Å / Num. obs: 11101 / % possible obs: 97.2 % / Redundancy: 6.6 % / Biso Wilson estimate: 13.08 Å2 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.03 / Rrim(I) all: 0.077 / Χ2: 0.954 / Net I/σ(I): 11 / Num. measured all: 73217 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OBH Resolution: 1.65→33.048 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.93 / 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: 45.42 Å2 / Biso mean: 16.9466 Å2 / Biso min: 5.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→33.048 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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