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- PDB-4hb5: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4hb5 | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR267. | ||||||
![]() | Engineered Protein | ||||||
![]() | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium (NESG) | ||||||
Function / homology | Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha![]() | ||||||
Biological species | artificial gene (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Computational design of self-assembling cyclic protein homo-oligomers. Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.1 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 438.1 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 18.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gmrC ![]() 4gpmSC ![]() 4hxtC ![]() 5hryC ![]() 5hrzC ![]() 5hs0C ![]() 5k7vC ![]() 5kbaC ![]() 5kwdC S: Starting model for refinement C: citing same article ( |
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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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | monomer,18.88 kD,98.5% |
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Components
#1: Protein | Mass: 18475.420 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) / Plasmid: OR267-21.1-SeM-R2 / Production host: ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.85 % |
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Crystal grow | Temperature: 277 K / Method: microbatch crystallization under oil / pH: 8 Details: 20% PEG 4000, 0.1M magnesium sulfate, 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: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 21, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97885 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 27096 / Num. obs: 26798 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 28.07 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 2.3→2.37 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 8.8 / Num. unique all: 2694 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GPM Resolution: 2.294→35.537 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.63 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 23.5 / 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: 30.706 Å2 / ksol: 0.343 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.8 Å2 / Biso mean: 39.025 Å2 / Biso min: 10.96 Å2
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Refinement step | Cycle: LAST / Resolution: 2.294→35.537 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: 9
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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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