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Yorodumi- PDB-4l7e: Three dimensional structure of mutant D78A of human HD domain-con... -
+Open data
-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 | ||||||
Components | HD domain-containing protein 2 | ||||||
Keywords | SIGNALING PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HDCC2 mutant D78A | ||||||
Function / homology | Function and homology information 5'-deoxynucleotidase / 5'-deoxynucleotidase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.229 Å | ||||||
Authors | 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) | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4l7e.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4l7e.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 4l7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/4l7e ftp://data.pdbj.org/pub/pdb/validation_reports/l7/4l7e | HTTPS FTP |
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-Related structure data
Related structure data | 4dmbSC 4l7wC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-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% |
-Components
#1: Protein | Mass: 23834.652 Da / Num. of mol.: 2 / Mutation: D78A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDDC2, C6orf74, NS5ATP2, CGI-130 / Plasmid: pET15_NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7Z4H3 #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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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 |