+Open data
-Basic information
Entry | Database: PDB / ID: 5b7j | ||||||
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Title | Structure model of Sap1-DNA complex | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / protein / DNA / interaction / complex / DNA BINDING PROTEIN-DNA complex | ||||||
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 | SOLUTION NMR / simulated annealing | ||||||
Authors | Jin, C. / Hu, Y. / Ding, J. / Zhang, Y. | ||||||
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 | 5b7j.cif.gz | 1022.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b7j.ent.gz | 889.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b7j ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b7j | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 13248.225 Da / Num. of mol.: 1 / Fragment: UNP residues 25-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: sap1, SPCC1672.02c / Production host: Escherichia coli (E. coli) / References: UniProt: P40847 |
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#2: DNA chain | Mass: 3638.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) |
#3: DNA chain | Mass: 3682.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast) |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 60 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 2 Details: The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter- ...Details: The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter-molecular distance restraints from NMR NOESY spectra. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |