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Yorodumi- PDB-4hhu: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hhu | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR280. | ||||||
Components | OR280 | ||||||
Keywords | Structural Genomics / Unknown Function / Engineered Protein / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Ribosomal protein S10 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / 3,6,9,12,15-PENTAOXAHEPTADECAN-1-OL Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. ...Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, 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 OR280. Authors: Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. ...Authors: Vorobiev, S. / Lew, S. / Lin, Y.-R. / Seetharaman, J. / Castelllanos, J. / Maglaqui, M. / Xiao, R. / Lee, D. / Koga, N. / Koga, R. / Everett, J.K. / Acton, T.B. / Baker, D. / 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 | 4hhu.cif.gz | 135.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hhu.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hhu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hhu_validation.pdf.gz | 686.4 KB | Display | wwPDB validaton report |
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Full document | 4hhu_full_validation.pdf.gz | 692.8 KB | Display | |
Data in XML | 4hhu_validation.xml.gz | 17 KB | Display | |
Data in CIF | 4hhu_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/4hhu ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hhu | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Details | monomer,24.34 kD,92.8% |
-Components
#1: Protein | Mass: 19490.471 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: OR280-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic #2: Chemical | ChemComp-AE4 / | #3: Chemical | #4: 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: 1.94 Å3/Da / Density % sol: 36.44 % |
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Crystal grow | Temperature: 277 K / Method: microbatch crystallization under oil / pH: 8 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 80% PEG 400, 0.1M Magnesium chloride, 0.1M Tris-HCl, pH 8.0., Microbatch crystallization ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 80% PEG 400, 0.1M Magnesium chloride, 0.1M Tris-HCl, pH 8.0., Microbatch crystallization under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97904 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97904 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 39520 / Num. obs: 39441 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3955 / % possible all: 97.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→31.812 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 0.82 / Phase error: 20.29 / 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: 60.014 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.73 Å2 / Biso mean: 30.69 Å2 / Biso min: 4.82 Å2
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Refinement step | Cycle: LAST / Resolution: 2→31.812 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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