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Yorodumi- PDB-3u0s: Crystal Structure of an Enzyme Redesigned Through Multiplayer Onl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u0s | ||||||
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Title | Crystal Structure of an Enzyme Redesigned Through Multiplayer Online Gaming: CE6 | ||||||
Components | Diisopropyl-fluorophosphatase | ||||||
Keywords | DE NOVO PROTEIN / HYDROLASE / protein engineering / computer-aided design / computationally-directed design / multiplayer online gaming / crowdsourcing / Foldit / Diels-Alder / enzyme design / active site redesign / substrate specificity / beta-propeller / helix-loop-helix / loop remodel | ||||||
Function / homology | Function and homology information diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding Similarity search - Function | ||||||
Biological species | Loligo vulgaris (squid) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å | ||||||
Authors | Bale, J.B. / Shen, B.W. / Stoddard, B.L. | ||||||
Citation | Journal: Nat.Biotechnol. / Year: 2012 Title: Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Authors: Eiben, C.B. / Siegel, J.B. / Bale, J.B. / Cooper, S. / Khatib, F. / Shen, B.W. / Players, F. / Stoddard, B.L. / Popovic, Z. / Baker, D. #1: Journal: Science / Year: 2010 Title: Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Authors: Siegel, J.B. / Zanghellini, A. / Lovick, H.M. / Kiss, G. / Lambert, A.R. / St Clair, J.L. / Gallaher, J.L. / Hilvert, D. / Gelb, M.H. / Stoddard, B.L. / Houk, K.N. / Michael, F.E. / Baker, D. #2: Journal: Structure / Year: 2001 Title: Crystal structure of diisopropylfluorophosphatase from Loligo vulgaris. Authors: Scharff, E.I. / Koepke, J. / Fritzsch, G. / Lucke, C. / Ruterjans, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u0s.cif.gz | 285.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u0s.ent.gz | 233.6 KB | Display | PDB format |
PDBx/mmJSON format | 3u0s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/3u0s ftp://data.pdbj.org/pub/pdb/validation_reports/u0/3u0s | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 37442.449 Da / Num. of mol.: 2 Mutation: E21T, I72S, A74I, N120A, D121Y, Y144F, R146I, M148L, Q149R, F173C, N175A, T195Q, E225K, D229A, S271A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loligo vulgaris (squid) / Gene: DFPASE / Plasmid: pET29b+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIG4, diisopropyl-fluorophosphatase |
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-Non-polymers , 5 types, 256 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | RESIDUES 36-44 (AMINO ACIDS PEVEVNGKP) OF THE WILD-TYPE REFERENCE PROTEIN Q7SIG4 WERE REPLACED WITH ...RESIDUES 36-44 (AMINO ACIDS PEVEVNGKP) OF THE WILD-TYPE REFERENCE PROTEIN Q7SIG4 WERE REPLACED WITH A COMPLETELY |
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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: 4.13 Å3/Da / Density % sol: 70.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 2% v/v PEG-400, 2.0M (NH4)2SO4; 25mM HEPES pH 7.25, 100mM NaCl, 5% glycerol (mother liquor); A solution was prepared of CE6 (15mg/ml) in protein buffer with a 1:10,000 ...Details: 100mM HEPES pH 7.5, 2% v/v PEG-400, 2.0M (NH4)2SO4; 25mM HEPES pH 7.25, 100mM NaCl, 5% glycerol (mother liquor); A solution was prepared of CE6 (15mg/ml) in protein buffer with a 1:10,000 molar ratio of Bovine Pancreatic Trypsin (Sigma T1426) added about 25 minutes prior to setting drops (protein buffer), VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→50 Å / Num. all: 37384 / Num. obs: 37384 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.07 / Χ2: 1.016 / Net I/σ(I): 20.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 38.17 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.198 / WRfactor Rwork: 0.1705 / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.8737 / SU B: 14.251 / SU ML: 0.139 / SU R Cruickshank DPI: 0.2962 / SU Rfree: 0.2083 / Cross valid method: THROUGHOUT / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 147.09 Å2 / Biso mean: 44.9428 Å2 / Biso min: 26.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→46.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.598→2.666 Å / Total num. of bins used: 20
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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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