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- PDB-2ivk: Crystal structure of the periplasmic endonuclease Vvn complexed w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ivk | ||||||
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Title | Crystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA | ||||||
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![]() | HYDROLASE / DNASE / ENDONUCLEASE / DNA HYDROLYSIS / PROTEIN NUCLEIC ACID INTERACTIONS / DNA CLEAVAGE PREFERENCE | ||||||
Function / homology | Endonuclease I / Endonuclease I / His-Me finger superfamily / endonuclease activity / metal ion binding / DNA / DNA (> 10) / Endonuclease I![]() | ||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.T. / Yang, W.J. / Li, C.L. / Doudeva, L.G. / Yuan, H.S. | ||||||
![]() | ![]() Title: Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases. Authors: Wang, Y.T. / Yang, W.J. / Li, C.L. / Doudeva, L.G. / Yuan, H.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 | ![]() | 232.9 KB | Display | ![]() |
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PDB format | ![]() | 181.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 489.3 KB | Display | ![]() |
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Full document | ![]() | 548.5 KB | Display | |
Data in XML | ![]() | 41.5 KB | Display | |
Data in CIF | ![]() | 57.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ivhC ![]() 1oupS 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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Unit cell |
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Components
#1: Protein | Mass: 24751.709 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q7MHK3, Hydrolases; Acting on ester bonds #2: DNA chain | Mass: 4608.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #3: DNA chain | Mass: 4567.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: DNA chain | Mass: 4897.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, HIS 80 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 80 TO ALA ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.34 % |
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Crystal grow | pH: 7 Details: 20% PEG3350, 0.2 M DI-SODIUM TARTRATE DEHYDRATE, pH 7.00 |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Dec 17, 2005 / Details: MIRRORS |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→37.09 Å / Num. obs: 24597 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 83.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OUP Resolution: 2.9→37.09 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 186489.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.9015 Å2 / ksol: 0.271852 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.9→37.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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