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Open data
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Basic information
Entry | Database: PDB / ID: 2vf8 | ||||||
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Title | Crystal structure of UvrA2 from Deinococcus radiodurans | ||||||
![]() | EXCINUCLEASE ABC SUBUNIT A | ||||||
![]() | DNA BINDING PROTEIN / NUCLEOTIDE-BINDING / ZINC-BINDING DOMAIN / SOS RESPONSE / METAL-BINDING / EXCISION NUCLEASE / ZINC-FINGER / ATP-BINDING / DNA-BINDING / DNA EXCISION / ZINC / CYTOPLASM / DNA DAMAGE / DNA REPAIR / ABC PROTEIN / DNA-BINDING PROTEIN | ||||||
Function / homology | ![]() excinuclease repair complex / nuclease activity / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Timmins, J. / Gordon, E. / Caria, S. / Leonard, G. / Kuo, M.S. / Monchois, V. / McSweeney, S. | ||||||
![]() | ![]() Title: Structural and Mutational Analyses of Deinococcus Radiodurans Uvra2 Provide Insight Into DNA Binding and Damage Recognition by Uvras. Authors: Timmins, J. / Gordon, E. / Caria, S. / Leonard, G. / Acajjaoui, S. / Kuo, M.S. / Monchois, V. / Mcsweeney, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 326.5 KB | Display | ![]() |
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PDB format | ![]() | 262.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 69.4 KB | Display | |
Data in CIF | ![]() | 92.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vf7SC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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2 | ![]()
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3 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.249, 0.906, -0.342), Vector: |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 91664.555 Da / Num. of mol.: 2 / Fragment: RESIDUES 81-922 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PLX02 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 119 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PO4 / | #6: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 65.86 % / Description: NONE |
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Crystal grow | pH: 5.2 Details: 17% PEG 3000, 0.1M CITRATE PH 5.2, 125MM AMMONIUM SULPHATE AND 1MM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2825 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 50546 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 3→3.2 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.1 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2VF7 Resolution: 3→102.06 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.871 / SU B: 41.8 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.471 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.55 Å2
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Refinement step | Cycle: LAST / Resolution: 3→102.06 Å
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Refine LS restraints |
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