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Yorodumi- PDB-4c30: Crystal structure of Deinococcus radiodurans UvrD in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c30 | ||||||
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Title | Crystal structure of Deinococcus radiodurans UvrD in complex with DNA, form 2 | ||||||
Components |
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Keywords | HYDROLASE/DNA / HYDROLASE-DNA COMPLEX / DNA REPAIR / DNA HELICASES / NUCLEOTIDE EXCISION REPAIR | ||||||
Function / homology | Function and homology information DNA helicase complex / recombinational repair / DNA 3'-5' helicase / 3'-5' DNA helicase activity / isomerase activity / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | DEINOCOCCUS RADIODURANS (radioresistant) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Stelter, M. / Acajjaoui, S. / McSweeney, S. / Timmins, J. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Structural and Mechanistic Insight Into DNA Unwinding by Deinococcus Radiodurans Uvrd. Authors: Stelter, M. / Acajjaoui, S. / Mcsweeney, S. / Timmins, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c30.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4c30.ent.gz | 925.1 KB | Display | PDB format |
PDBx/mmJSON format | 4c30.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c30_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4c30_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4c30_validation.xml.gz | 115.4 KB | Display | |
Data in CIF | 4c30_validation.cif.gz | 153.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c3/4c30 ftp://data.pdbj.org/pub/pdb/validation_reports/c3/4c30 | HTTPS FTP |
-Related 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ADFI
#1: Protein | Mass: 74100.484 Da / Num. of mol.: 4 / Fragment: C-TERMINAL TRUNCATION, RESIDUES 1-665 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant) Plasmid: PET151D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RTI9, DNA helicase |
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-DNA chain , 2 types, 4 molecules KXLY
#2: DNA chain | Mass: 7677.927 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 7615.906 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) |
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-Non-polymers , 3 types, 105 molecules
#4: Chemical | #5: Chemical | ChemComp-MG / #6: 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: 2.75 Å3/Da / Density % sol: 60.02 % / Description: NONE |
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Crystal grow | Details: 22% PEG 3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.1 M NA-FLUORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.078 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.078 Å / Relative weight: 1 |
Reflection | Resolution: 3→66.2 Å / Num. obs: 62649 / % possible obs: 89 % / Redundancy: 1.5 % / Biso Wilson estimate: 72.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 1.9 / % possible all: 86.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DRUVRD FORM1 Resolution: 3→66.18 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.889 / SU B: 57.527 / SU ML: 0.486 / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 104.631 Å2
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Refinement step | Cycle: LAST / Resolution: 3→66.18 Å
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Refine LS restraints |
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