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Yorodumi- PDB-3u26: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u26 | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR48 | ||||||
Components | PF00702 domain protein | ||||||
Keywords | Structural Genomics / Unknown Function / PSI-Biology / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Function and homology information small molecule biosynthetic process / cellular biosynthetic process / organonitrogen compound biosynthetic process / phosphatase activity Similarity search - Function | ||||||
Biological species | Pyrococcus horikoshii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å | ||||||
Authors | Seetharaman, J. / Lew, S. / Nivon, L. / Baker, D. / Bjelic, S. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Everett, J.K. / Acton, T.B. ...Seetharaman, J. / Lew, S. / Nivon, L. / Baker, D. / Bjelic, S. / Ciccosanti, C. / Sahdev, S. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction. Authors: Bjelic, S. / Nivon, L.G. / Celebi-Olcum, N. / Kiss, G. / Rosewall, C.F. / Lovick, H.M. / Ingalls, E.L. / Gallaher, J.L. / Seetharaman, J. / Lew, S. / Montelione, G.T. / Hunt, J.F. / Michael, ...Authors: Bjelic, S. / Nivon, L.G. / Celebi-Olcum, N. / Kiss, G. / Rosewall, C.F. / Lovick, H.M. / Ingalls, E.L. / Gallaher, J.L. / Seetharaman, J. / Lew, S. / Montelione, G.T. / Hunt, J.F. / Michael, F.E. / Houk, K.N. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u26.cif.gz | 59.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u26.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 3u26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u2/3u26 ftp://data.pdbj.org/pub/pdb/validation_reports/u2/3u26 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26933.738 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pet21 / Production host: Escherichia coli (E. coli) / References: UniProt: O58216*PLUS |
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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: 1.92 Å3/Da / Density % sol: 35.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M PBS buffer pH 7.5 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, 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 4r / Detector: CCD / Date: Aug 10, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→50 Å / Num. obs: 27144 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.04 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.128 / Num. unique all: 3628 / % possible all: 69 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.59→45.49 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.919 / SU B: 1.952 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.609 Å2
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Refinement step | Cycle: LAST / Resolution: 1.59→45.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.592→1.633 Å / Total num. of bins used: 20
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