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Yorodumi- PDB-2vld: crystal structure of a repair endonuclease from Pyrococcus abyssi -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vld | ||||||
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Title | crystal structure of a repair endonuclease from Pyrococcus abyssi | ||||||
Components | Endonuclease NucS | ||||||
Keywords | HYDROLASE / ENDONUCLEASE | ||||||
Function / homology | Function and homology information single-stranded DNA endodeoxyribonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Pyrococcus abyssi (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å | ||||||
Authors | Ren, B. / Kuhn, J. / Meslet-Cladiere, L. / Briffotaux, J. / Norais, C. / Lavigne, R. / Flament, D. / Ladenstein, R. / Myllykallio, H. | ||||||
Citation | Journal: EMBO J. / Year: 2009 Title: Structure and function of a novel endonuclease acting on branched DNA substrates. Authors: Ren, B. / Kuhn, J. / Meslet-Cladiere, L. / Briffotaux, J. / Norais, C. / Lavigne, R. / Flament, D. / Ladenstein, R. / Myllykallio, H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vld.cif.gz | 102 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vld.ent.gz | 84.5 KB | Display | PDB format |
PDBx/mmJSON format | 2vld.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vl/2vld ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vld | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 29151.902 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: nucS, PYRAB01260, PAB2263 / Cell line (production host): CodonPlus-RIL / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlus-RIL References: UniProt: Q9V2E8, Hydrolases; Acting on ester bonds #2: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, ILE 89 TO MSE ENGINEERED RESIDUE IN CHAIN A, LEU 188 TO MSE ...ENGINEERED | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9077 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 22, 2006 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9077 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. obs: 19639 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 37.3 |
Reflection shell | Resolution: 2.6→2.7 Å / Redundancy: 3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.941 / SU B: 28.058 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.713 / ESU R Free: 0.3 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.65 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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