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- PDB-4l1j: Three dimensional structure of mutant D143A of human HD domain-co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l1j | ||||||
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Title | Three dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723 | ||||||
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![]() | HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HDCC2 / Hepatitis C virus NS5A-transactivated protein 2 / NS5ATP2 | ||||||
Function / homology | ![]() 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, O. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. ...Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, O. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Three dimensional structure of mutant D143A of human HD domain-containing protein 2, Northeast Structural Genomics Consortium (NESG) Target HR6723 Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, O. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 182.7 KB | Display | ![]() |
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PDB format | ![]() | 145.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 683.8 KB | Display | ![]() |
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Full document | ![]() | 686.5 KB | Display | |
Data in XML | ![]() | 18.6 KB | Display | |
Data in CIF | ![]() | 26.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dmbS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | dimer,61.27 kD,68.3% |
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Components
#1: Protein | Mass: 23754.674 Da / Num. of mol.: 1 / Mutation: D143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
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#2: Protein | Mass: 23834.652 Da / Num. of mol.: 1 / Mutation: D143A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-PE4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:Na2H2PO4 0.1M, MES 0.1M, PEG400 40%, microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 14, 2013 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 42001 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 47 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 4DMB Resolution: 1.824→35.383 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.16 / σ(F): 1.44 / Phase error: 19.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.824→35.383 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -20.048 Å / Origin y: -12.9506 Å / Origin z: 15.7411 Å
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Refinement TLS group | Selection details: all |