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- PDB-3scx: RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3scx | ||||||
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Title | RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+ | ||||||
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![]() | TRANSFERASE/DNA / DNA binding / TRANSFERASE-DNA complex | ||||||
Function / homology | ![]() bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity ...bidirectional double-stranded viral DNA replication / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / nucleotide-excision repair, DNA gap filling / DNA replication proofreading / 3'-5'-DNA exonuclease activity / SOS response / 3'-5' exonuclease activity / base-excision repair, gap-filling / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / nucleotide binding / DNA binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, M. / Wang, J. / Konigsberg, W.H. | ||||||
![]() | ![]() Title: Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase. Authors: Xia, S. / Wang, M. / Blaha, G. / Konigsberg, W.H. / Wang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 418.2 KB | Display | ![]() |
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PDB format | ![]() | 336.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 820.7 KB | Display | ![]() |
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Full document | ![]() | 841.7 KB | Display | |
Data in XML | ![]() | 38.3 KB | Display | |
Data in CIF | ![]() | 55.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3s9hC ![]() 3si6C ![]() 3sjjC ![]() 3snnC ![]() 3spyC ![]() 3spzC ![]() 3sq0C ![]() 3sq1C ![]() 1ig9S 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
-DNA chain , 2 types, 2 molecules TP
#1: DNA chain | Mass: 5525.592 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: template DNA strand |
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#2: DNA chain | Mass: 3967.585 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: primer DNA strand |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 104446.938 Da / Num. of mol.: 1 / Mutation: D222A,D327A,L561A,S565G,Y567A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 350 molecules ![](data/chem/img/DUP.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-DUP / | ||
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#5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.08 % |
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Crystal grow | Temperature: 293.15 K / Method: microbatch vapor diffusion / pH: 6.5 Details: 150 mM calcium chloride, 1% w/v PEG350 MME, 100 mM sodium cacodylate, pH 6.5, MICROBATCH VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007 / Details: mirrors |
Radiation | Monochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→100 Å / Num. all: 49563 / Num. obs: 49563 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Biso Wilson estimate: 45 Å2 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.23 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.08 / Num. unique all: 4897 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IG9 Resolution: 2.35→88.04 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 21.276 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.404 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : RESIDUAL ONLY
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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: 43.388 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→88.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 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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