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- PDB-6ur2: DNA polymerase I Large Fragment from Bacillus stearothermophilus ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ur2 | ||||||
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Title | DNA polymerase I Large Fragment from Bacillus stearothermophilus with DNA template and primer containing an N3'-> P5' linkage | ||||||
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![]() | REPLICATION/DNA / NP linkage / DNA polymerase / REPLICATION-DNA complex | ||||||
Function / homology | ![]() double-strand break repair via alternative nonhomologous end joining / 3'-5' exonuclease activity / DNA-templated DNA replication / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, W. / Lelyveld, V.S. / Szostak, J.W. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase. Authors: Lelyveld, V.S. / Zhang, W. / Szostak, J.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.1 KB | Display | ![]() |
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PDB format | ![]() | 108.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
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Full document | ![]() | 449.6 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 32 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ur4C ![]() 6ur9C ![]() 6us5C ![]() 1l5uS 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: 66101.766 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: Strain X / Gene: DPO1, polA / Production host: ![]() ![]() |
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#2: DNA chain | Mass: 3069.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: DNA chain | Mass: 3647.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 61.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10mM MgCl2, 0.8 M Succinic acid pH 7.0 |
-Data collection
Diffraction | Mean temperature: 99 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→50 Å / Num. obs: 39951 / % possible obs: 99.9 % / Redundancy: 8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.046 / Rrim(I) all: 0.129 / Χ2: 1.312 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 8 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 3928 / CC1/2: 0.986 / Rpim(I) all: 0.192 / Rrim(I) all: 0.543 / Χ2: 0.986 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1L5U Resolution: 2.27→40.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.508 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.238 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 148.36 Å2 / Biso mean: 42.616 Å2 / Biso min: 23.69 Å2
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Refinement step | Cycle: final / Resolution: 2.27→40.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.272→2.331 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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