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Open data
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Basic information
Entry | Database: PDB / ID: 3gp8 | ||||||
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Title | Crystal structure of the binary complex of RecD2 with DNA | ||||||
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![]() | HYDROLASE/DNA / ALPHA AND BETA PROTEIN / ATP-BINDING / NUCLEOTIDE-BINDING / HELICASE / HYDROLASE-DNA COMPLEX | ||||||
Function / homology | ![]() exodeoxyribonuclease V complex / DNA 5'-3' helicase / single-stranded DNA helicase activity / ATP-dependent activity, acting on DNA / isomerase activity / 5'-3' DNA helicase activity / DNA recombination / ATP hydrolysis activity / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Saikrishnan, K. / Cook, N. / Wigley, D.B. | ||||||
![]() | ![]() Title: Mechanistic basis of 5'-3' translocation in SF1B helicases. Authors: Saikrishnan, K. / Powell, B. / Cook, N.J. / Webb, M.R. / Wigley, D.B. #1: ![]() Title: DNA binding to RecD: role of the 1B domain in SF1B helicase activity. Authors: Saikrishnan, K. / Griffiths, S.P. / Cook, N. / Court, R. / Wigley, D.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.4 KB | Display | ![]() |
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PDB format | ![]() | 92.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.2 KB | Display | ![]() |
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Full document | ![]() | 448.9 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 33.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gplC ![]() 3e1sS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 61465.914 Da / Num. of mol.: 1 / Fragment: UNP residues 151-715 Source method: isolated from a genetically manipulated source Details: N-terminus deletion mutant of RecD2 Source: (gene. exp.) ![]() Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279 / Gene: DR_1902, recD / Plasmid: pET22b / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 4213.742 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic DNA |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.52 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 15% PEG 8000, 2-6% Ethylene glycol, 100mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2008 / Details: mirrors |
Radiation | Monochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 24877 / Num. obs: 24589 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.032 / Rsym value: 0.032 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2.5→2.6 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 8 / Num. unique all: 2492 / Rsym value: 0.175 / % possible all: 91.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3E1S Resolution: 2.5→45.18 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.905 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.519 / ESU R Free: 0.299 / 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: 37.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.18 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.57 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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