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Yorodumi- PDB-5jdk: Crystal structure of the DNA binding domain of Sap1 in fission ye... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5jdk | |||||||||
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Title | Crystal structure of the DNA binding domain of Sap1 in fission yeast S.pombe | |||||||||
Components | Switch-activating protein 1 | |||||||||
Keywords | DNA BINDING PROTEIN / DNA replication / alpha-helix | |||||||||
Function / homology | Function and homology information site-specific DNA replication termination / mitotic pre-replicative complex assembly / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / gene conversion at mating-type locus / DNA binding, bending / chromosome segregation / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromatin ...site-specific DNA replication termination / mitotic pre-replicative complex assembly / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / gene conversion at mating-type locus / DNA binding, bending / chromosome segregation / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromatin / DNA binding / nucleus Similarity search - Function | |||||||||
Biological species | Schizosaccharomyces pombe (fission yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.998 Å | |||||||||
Authors | He, P. / Wang, T. | |||||||||
Funding support | China, 2items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe. Authors: Guan, L. / He, P. / Yang, F. / Zhang, Y. / Hu, Y. / Ding, J. / Hua, Y. / Zhang, Y. / Ye, Q. / Hu, J. / Wang, T. / Jin, C. / Kong, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jdk.cif.gz | 80.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jdk.ent.gz | 60.2 KB | Display | PDB format |
PDBx/mmJSON format | 5jdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/5jdk ftp://data.pdbj.org/pub/pdb/validation_reports/jd/5jdk | HTTPS FTP |
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-Related 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: 16156.630 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast) Strain: 972 / ATCC 24843 / Gene: sap1, SPCC1672.02c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40847 |
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#2: Chemical | ChemComp-GOL / |
#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: 1.63 Å3/Da / Density % sol: 24.75 % / Description: hexagonal prism, Rod |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.8 Details: 200mM Trimethylamine N-oxide, 15-22% (w/v) PEG 2000MME |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Entry-ID: 5JDK
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Reflection shell | Resolution: 0.998→1.034 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 1.22 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 0.998→17.87 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 17.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.998→17.87 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: -21.3255 Å / Origin y: 1.9302 Å / Origin z: 79.2675 Å
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Refinement TLS group | Selection details: chain 'A' |