+Open data
-Basic information
Entry | Database: PDB / ID: 3ulp | ||||||
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Title | Plasmodium falciparum SSB complex with ssDNA | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / OB-fold / DNA binding / single-stranded DNA / apicoplast / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information positive regulation of helicase activity / apicoplast / mitochondrial DNA replication / nucleoid / mitochondrial nucleoid / single-stranded DNA binding / mitochondrion Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) Synthetic DNA (others) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Antony, E. / Lohman, T.M. / Korolev, S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2012 Title: Plasmodium falciparum SSB Tetramer Wraps Single-Stranded DNA with Similar Topology but Opposite Polarity to E. coli SSB. Authors: Antony, E. / Weiland, E.A. / Korolev, S. / Lohman, T.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ulp.cif.gz | 132 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ulp.ent.gz | 102.9 KB | Display | PDB format |
PDBx/mmJSON format | 3ulp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ulp_validation.pdf.gz | 473.4 KB | Display | wwPDB validaton report |
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Full document | 3ulp_full_validation.pdf.gz | 499.4 KB | Display | |
Data in XML | 3ulp_validation.xml.gz | 25.3 KB | Display | |
Data in CIF | 3ulp_validation.cif.gz | 35.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/3ulp ftp://data.pdbj.org/pub/pdb/validation_reports/ul/3ulp | HTTPS FTP |
-Related structure data
Related structure data | 1eqqS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 14636.719 Da / Num. of mol.: 4 / Fragment: UNP residues 77-200 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PFE0435c / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I415 #2: DNA chain | Mass: 10601.791 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic DNA (others) #3: Water | ChemComp-HOH / | |
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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: 2.64 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Bis-Tris Propane, pH 8.5, 20 % PEG 3350, 0.2 M sodium bromide, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 21, 2011 |
Radiation | Monochromator: VHF optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 48456 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2375 / % possible all: 97.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EQQ Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 5.001 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.239 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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