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Yorodumi- PDB-4ijb: Crystal Structure of Engineered Protein, Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ijb | ||||||
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Title | Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR288 | ||||||
Components | Engineered Protein OR288 | ||||||
Keywords | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Engineered Protein | ||||||
Function / homology | Aldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta Function and homology information | ||||||
Biological species | artificial gene (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.739 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Bick, M.J. / Seetharaman, J. / Khare, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Day, A. / Everett, J.K. ...Vorobiev, S. / Su, M. / Bick, M.J. / Seetharaman, J. / Khare, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Day, A. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Hunt, J. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Engineered Protein OR288. Authors: Vorobiev, S. / Su, M. / Bick, M.J. / Seetharaman, J. / Khare, S. / Maglaqui, M. / Xiao, R. / Lee, D. / Day, A. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Hunt, J. / Tong, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ijb.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ijb.ent.gz | 90 KB | Display | PDB format |
PDBx/mmJSON format | 4ijb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ijb_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 4ijb_full_validation.pdf.gz | 425.3 KB | Display | |
Data in XML | 4ijb_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 4ijb_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ijb ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ijb | HTTPS FTP |
-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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Details | monomer,26.36 kD,97.4% |
-Components
#1: Protein | Mass: 29858.168 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) / Plasmid: OR288-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic |
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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: 1.97 Å3/Da / Density % sol: 37.49 % |
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Crystal grow | Temperature: 277 K / Method: microbatch crystallization under oil / pH: 6.5 Details: 30% PEG 8000, 0.2M sodium acetate, 0.1M sodium cacodylate, pH 6.5, Microbatch crystallization under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97921 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 |
Reflection | Resolution: 1.739→40.58 Å / Num. all: 46740 / Num. obs: 46740 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.739→1.85 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.949 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.739→25.499 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.41 / σ(F): 1.21 / Phase error: 18.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.591 Å2 / ksol: 0.428 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.739→25.499 Å
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Refine LS restraints |
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LS refinement shell |
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