+Open data
-Basic information
Entry | Database: PDB / ID: 2is1 | ||||||
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Title | Crystal structure of UvrD-DNA-SO4 complex | ||||||
Components |
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Keywords | HYDROLASE/DNA / DNA helicase / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / nucleotide-excision repair, DNA duplex unwinding / DNA 3'-5' helicase / DNA translocase activity / single-stranded DNA helicase activity / recombinational repair / SOS response ...rolling circle DNA replication / single-stranded DNA-dependent ATP-dependent DNA helicase complex / DNA helicase complex / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / nucleotide-excision repair, DNA duplex unwinding / DNA 3'-5' helicase / DNA translocase activity / single-stranded DNA helicase activity / recombinational repair / SOS response / 3'-5' DNA helicase activity / DNA duplex unwinding / replication fork processing / DNA unwinding involved in DNA replication / mismatch repair / isomerase activity / DNA helicase activity / nucleotide-excision repair / response to radiation / ATP hydrolysis activity / protein homodimerization activity / DNA binding / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Yang, W. / Lee, J.Y. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2006 Title: UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke. Authors: Lee, J.Y. / Yang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2is1.cif.gz | 285.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2is1.ent.gz | 222.8 KB | Display | PDB format |
PDBx/mmJSON format | 2is1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/is/2is1 ftp://data.pdbj.org/pub/pdb/validation_reports/is/2is1 | HTTPS FTP |
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-Related structure data
Related structure data | 2is2C 2is4C 2is6C 2pjrS 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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2 |
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Unit cell |
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-Components
-DNA chain , 2 types, 4 molecules CEDF
#1: DNA chain | Mass: 5190.353 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3029.994 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 77797.078 Da / Num. of mol.: 2 / Mutation: A399V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: uvrD / Production host: Escherichia coli (E. coli) References: UniProt: P03018, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
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-Non-polymers , 4 types, 65 molecules
#4: Chemical | ChemComp-HG / #5: Chemical | #6: Chemical | #7: 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: 2.85 Å3/Da / Density % sol: 56.79 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG 3350, Sodium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Components of the solutions |
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-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: Oct 25, 2004 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 48424 / Num. obs: 48037 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 115.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.17 / Num. unique all: 4390 / % possible all: 92.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry: 2PJR Resolution: 2.9→29.76 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 207043.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.8398 Å2 / ksol: 0.314594 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 57 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→29.76 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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