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- PDB-4f2v: Crystal Structure of de novo designed serine hydrolase, Northeast... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4f2v | ||||||
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Title | Crystal Structure of de novo designed serine hydrolase, Northeast Structural Genomics Consortium (NESG) Target OR165 | ||||||
![]() | De novo designed serine hydrolase | ||||||
![]() | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / de novo design | ||||||
Function / homology | ![]() thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / response to radiation / regulation of translation / methylation / magnesium ion binding / protein homodimerization activity / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | artificial gene (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Maglaqui, M. / Xiao, R. / Kohan, E. / Rajagopalan, S. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Design of activated serine-containing catalytic triads with atomic-level accuracy. Authors: Rajagopalan, S. / Wang, C. / Yu, K. / Kuzin, A.P. / Richter, F. / Lew, S. / Miklos, A.E. / Matthews, M.L. / Seetharaman, J. / Su, M. / Hunt, J.F. / Cravatt, B.F. / 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 | ![]() | 230.3 KB | Display | ![]() |
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PDB format | ![]() | 184.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 825.3 KB | Display | ![]() |
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Full document | ![]() | 834.7 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 30.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3tp4C ![]() 3v45C ![]() 4drtC ![]() 4essC ![]() 4etjC ![]() 4etkC ![]() 4jcaC ![]() 4jllC ![]() 4jvvC ![]() 1bq2S 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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Unit cell |
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Details | dimer,62.32 kD,98.1% |
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Components
#1: Protein | Mass: 31624.697 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) artificial gene (others) / Plasmid: pet29b / Production host: ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution:20% PEG 4000, 0.5% Dodecyl D-maltoside, 0.2M MgCl2, 0.1M TRIS, VAPOR DIFFUSION, SITTING DROP, 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: May 1, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 19218 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 35.11 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BQ2 Resolution: 2.493→47.663 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.814 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.75 / 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: 26.665 Å2 / ksol: 0.336 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 238.95 Å2 / Biso mean: 38.674 Å2 / Biso min: 11.49 Å2
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Refinement step | Cycle: LAST / Resolution: 2.493→47.663 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: 7
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Refinement TLS params. | Method: refined / Origin x: 11.5495 Å / Origin y: 2.3572 Å / Origin z: 14.1045 Å
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Refinement TLS group |
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