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Yorodumi- PDB-4pq8: Crystal Structure of Engineered Protein, Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pq8 | ||||||
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Title | Crystal Structure of Engineered Protein, Northeast Structural Genomics Consortium Target OR465 | ||||||
Components | DESIGNED PROTEIN OR465Design | ||||||
Keywords | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta Function and homology information | ||||||
Biological species | SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.833 Å | ||||||
Authors | Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. ...Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Engineered Protein OR465. Authors: Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pq8.cif.gz | 107.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pq8.ent.gz | 80.9 KB | Display | PDB format |
PDBx/mmJSON format | 4pq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/4pq8 ftp://data.pdbj.org/pub/pdb/validation_reports/pq/4pq8 | HTTPS FTP |
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-Related structure data
Related structure data | 3rfjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | monomer,31.3 kD,96.8% |
-Components
#1: Protein | Mass: 30077.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: OR465-15.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic |
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#2: Chemical | ChemComp-CL / |
#3: 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: 2.27 Å3/Da / Density % sol: 45.77 % |
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Crystal grow | Temperature: 291 K / Method: microbatch crystallization under oil / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 40% PEG 4000, 0.1M potassium phosphate monobasic, 0.1M MES, pH 6.0, Microbatch ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Crystallization cocktail: 40% PEG 4000, 0.1M potassium phosphate monobasic, 0.1M MES, pH 6.0, Microbatch crystallization under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 26, 2014 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97908 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→50 Å / Num. all: 23943 / Num. obs: 23751 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 16.46 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 48.6 |
Reflection shell | Resolution: 1.83→1.9 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 10 / Num. unique all: 2367 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3RFJ Resolution: 1.833→41.97 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 16.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.025 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.82 Å2 / Biso mean: 22.045 Å2 / Biso min: 5.6 Å2
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Refinement step | Cycle: LAST / Resolution: 1.833→41.97 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: 17
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Refinement TLS params. | Method: refined / Origin x: 36.5882 Å / Origin y: 10.4612 Å / Origin z: 0.0628 Å
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Refinement TLS group | Selection details: chain A |