+Open data
-Basic information
Entry | Database: PDB / ID: 4pog | ||||||
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Title | MCM-ssDNA co-crystal structure | ||||||
Components |
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Keywords | REPLICATION / DNA BINDING PROTEIN/DNA / OB-fold / DNA replication / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information single-stranded 3'-5' DNA helicase activity / MCM complex / intein-mediated protein splicing / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / endonuclease activity / DNA helicase / cell division / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.203 Å | ||||||
Authors | Froelich, C.A. / Kang, S. / Epling, L.B. / Bell, S.P. / Enemark, E.J. | ||||||
Citation | Journal: Elife / Year: 2014 Title: A conserved MCM single-stranded DNA binding element is essential for replication initiation. Authors: Froelich, C.A. / Kang, S. / Epling, L.B. / Bell, S.P. / Enemark, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pog.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4pog.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 4pog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pog_validation.pdf.gz | 570 KB | Display | wwPDB validaton report |
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Full document | 4pog_full_validation.pdf.gz | 655.2 KB | Display | |
Data in XML | 4pog_validation.xml.gz | 109.5 KB | Display | |
Data in CIF | 4pog_validation.cif.gz | 145.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/po/4pog ftp://data.pdbj.org/pub/pdb/validation_reports/po/4pog | HTTPS FTP |
-Related structure data
Related structure data | 4pofSC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 0 - 254 / Label seq-ID: 1 - 255
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-Components
#1: Protein | Mass: 29400.711 Da / Num. of mol.: 12 / Fragment: N-terminal domain (UNP residues 2-256) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: Cdc21, PF0482 / Plasmid: pRSFduet pLE009.3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: Q8U3I4 #2: DNA chain | Mass: 9080.827 Da / Num. of mol.: 4 / Source method: obtained synthetically #3: Chemical | ChemComp-ZN / |
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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: 2.65 Å3/Da / Density % sol: 53.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 50 mM MES, pH 6.0, 10 mM magnesium acetate, 28.5% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 30, 2010 |
Radiation | Monochromator: Rosenbaum-Rock double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.203→50 Å / Num. all: 66924 / Num. obs: 66920 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3.203→3.31 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.786 / Mean I/σ(I) obs: 1.64 / Num. unique all: 6626 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4POF Resolution: 3.203→48.51 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.869 / SU B: 80.109 / SU ML: 0.585 / Cross valid method: THROUGHOUT / ESU R Free: 0.601 / 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: 129.847 Å2
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Refinement step | Cycle: LAST / Resolution: 3.203→48.51 Å
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Refine LS restraints |
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