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Yorodumi- PDB-4dmb: X-ray structure of human hepatitus C virus NS5A-transactivated pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dmb | ||||||
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Title | X-ray structure of human hepatitus C virus NS5A-transactivated protein 2 at the resolution 1.9A, Northeast Structural Genomics Consortium (NESG) Target HR6723 | ||||||
Components | HD domain-containing protein 2 | ||||||
Keywords | IMMUNE SYSTEM / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) / HD domain-containing protein 2 / hepatitus C virus NS5A-transactivated protein 2 / HCV NS5A-transactivated protein 2 / Mitochondrial Protein Partnership / MPP | ||||||
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 / SAD / Resolution: 1.9 Å | ||||||
Authors | Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) / Mitochondrial Protein Partnership (MPP) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target HR6723 Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dmb.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dmb.ent.gz | 144.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dmb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dmb_validation.pdf.gz | 474.2 KB | Display | wwPDB validaton report |
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Full document | 4dmb_full_validation.pdf.gz | 475.2 KB | Display | |
Data in XML | 4dmb_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4dmb_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/4dmb ftp://data.pdbj.org/pub/pdb/validation_reports/dm/4dmb | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Dimer, or trimer,61.41 kD,74.7%, or heptamer,138.4 kD,19.4% |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23798.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: BL21(DE3)+ Magic / Gene: HDDC2, C6orf74, NS5ATP2, CGI-130 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Z4H3 |
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-Non-polymers , 7 types, 185 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #8: 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: 2.14 Å3/Da / Density % sol: 42.6 % |
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Crystal grow | Temperature: 293 K / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:Mg(NO3)2 0.1M, MES 0.1M, PEG4000 40% (w/v), microbatch under oil, temperature 293KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97906 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 1, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97906 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 59948 / % possible obs: 96.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.8 / % possible all: 71.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.9→42.295 Å / Occupancy max: 1 / Occupancy min: 0.65 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.583 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→42.295 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: 34.7794 Å / Origin y: 53.7885 Å / Origin z: 66.0152 Å
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Refinement TLS group | Selection details: all |