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Yorodumi- PDB-4diu: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4diu | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR94 | ||||||
Components | Engineered Protein PF00326Engineering | ||||||
Keywords | Structural Genomics / Unknown Function / PSI-Biology / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Seetharaman, J. / Lew, S. / Wang, D. / Kohan, E. / Patel, D. / Whitehead, T. / Fleishman, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. ...Seetharaman, J. / Lew, S. / Wang, D. / Kohan, E. / Patel, D. / Whitehead, T. / Fleishman, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR94 Authors: Seetharaman, J. / Lew, S. / Wang, D. / Kohan, E. / Patel, D. / Whitehead, T. / Fleishman, S. / Ciccosanti, C. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4diu.cif.gz | 62.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4diu.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 4diu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/4diu ftp://data.pdbj.org/pub/pdb/validation_reports/di/4diu | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28453.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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#2: Water | ChemComp-HOH / |
-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: 55.39 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6 Details: 2.03 M Lithium sulfate monohydrate .1M MES pH 6, Microbatch under oil, temperature 4 K, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 22, 2012 |
Radiation | Monochromator: Bent single crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 17960 / % possible obs: 92.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.8 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.66 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 213462.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 35.6666 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 29.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→30.66 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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