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- PDB-4psj: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4psj | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium (NESG) Target OR464. | ||||||
![]() | OR464 | ||||||
![]() | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Engineered Protein / NESG / OR464 / Northeast Structural Genomics Consortium | ||||||
Function / homology | Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Janjua, H. / Xiao, R. / Maglaqui, M. / Park, K. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / 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) | ||||||
![]() | ![]() Title: Crystal Structure of Engineered Protein OR464. Authors: Vorobiev, S. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.4 KB | Display | ![]() |
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PDB format | ![]() | 87.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 423.5 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rfjS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29894.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: OR464-15.1 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.1 % |
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Crystal grow | Temperature: 291 K / Method: microbatch crystallization under oil / pH: 5.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 25% PEG 3350, 0.1M Bis-Tris, Microbatch crystallization under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / 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: 0.97942 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 29867 / Num. obs: 28015 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.48 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 25.6 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2940 / % possible all: 68.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3RFJ Resolution: 1.992→31.911 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 27.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.167 Å2 / ksol: 0.306 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.96 Å2 / Biso mean: 33.483 Å2 / Biso min: 10.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.992→31.911 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: 10
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Refinement TLS params. | Method: refined / Origin x: 7.3419 Å / Origin y: 0.571 Å / Origin z: 7.0469 Å
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Refinement TLS group | Selection details: chain A |