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- PDB-4l7e: Three dimensional structure of mutant D78A of human HD domain-con... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4l7e | ||||||
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Title | Three dimensional structure of mutant D78A of human HD domain-containing protein 2, Genomics Consortium (NESG) Target HR6723 | ||||||
![]() | HD domain-containing protein 2 | ||||||
![]() | SIGNALING PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HDCC2 mutant D78A | ||||||
Function / homology | ![]() 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. ...Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / 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: Northeast Structural Genomics Consortium Target HR6723 Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Brown, G. / Flick, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Authors: Kuzin, A. / Su, M. / Yakunin, A. / Beloglazova, N. / 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) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 172.5 KB | Display | ![]() |
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PDB format | ![]() | 138.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.6 KB | Display | ![]() |
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Full document | ![]() | 452.2 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4dmbSC ![]() 4l7wC S: Starting model for refinement C: citing same article ( |
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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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1 |
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Unit cell |
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Details | dimer,44.42 kD,92.5% |
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Components
#1: Protein | Mass: 23834.652 Da / Num. of mol.: 2 / Mutation: D78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | Num. of mol.: 2 / Source method: obtained synthetically #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.23 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M LiCl, 0.1M sodium acetate, 40% PEG1000, microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2012 / Details: mirrors |
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: 2.2→50 Å / Num. obs: 24213 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 29.15 Å2 / Rmerge(I) obs: 0.092 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4DMB Resolution: 2.229→47.567 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.24 / σ(F): 1.44 / Phase error: 21.24 / 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: 41.102 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.229→47.567 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: 20.0149 Å / Origin y: 12.5146 Å / Origin z: 15.5944 Å
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Refinement TLS group | Selection details: all |