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Yorodumi- PDB-3u13: Crystal Structure of de Novo design of cystein esterase ECH13 at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u13 | ||||||
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Title | Crystal Structure of de Novo design of cystein esterase ECH13 at the resolution 1.6A, Northeast Structural Genomics Consortium Target OR51 | ||||||
Components | artificial protein OR51 | ||||||
Keywords | HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / ECH13 | ||||||
Function / homology | Function and homology information Deoxyribonucleotidase; domain 2 / Ribonucleotide Reductase Protein R1; domain 1 / HAD superfamily/HAD-like / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kohan, E. / Richter, F. / Everett, J.K. / Acton, T.B. / Baker, D. ...Kuzin, A. / Su, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Kohan, E. / Richter, F. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Authors: Richter, F. / Blomberg, R. / Khare, S.D. / Kiss, G. / Kuzin, A.P. / Smith, A.J. / Gallaher, J. / Pianowski, Z. / Helgeson, R.C. / Grjasnow, A. / Xiao, R. / Seetharaman, J. / Su, M. / ...Authors: Richter, F. / Blomberg, R. / Khare, S.D. / Kiss, G. / Kuzin, A.P. / Smith, A.J. / Gallaher, J. / Pianowski, Z. / Helgeson, R.C. / Grjasnow, A. / Xiao, R. / Seetharaman, J. / Su, M. / Vorobiev, S. / Lew, S. / Forouhar, F. / Kornhaber, G.J. / Hunt, J.F. / Montelione, G.T. / Tong, L. / Houk, K.N. / Hilvert, D. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u13.cif.gz | 109.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u13.ent.gz | 82.5 KB | Display | PDB format |
PDBx/mmJSON format | 3u13.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u13_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 3u13_full_validation.pdf.gz | 444 KB | Display | |
Data in XML | 3u13_validation.xml.gz | 12.5 KB | Display | |
Data in CIF | 3u13_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u13 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u13 | HTTPS FTP |
-Related structure data
Related structure data | 3u1oC 3u1vC 3uakC 1q92S S: Starting model for refinement C: citing same article (ref.) |
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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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Components on special symmetry positions |
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Details | authors indicate the biological unit as a trimer of 61.03 kD at 96.3% |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24193.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29b+ / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) |
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-Non-polymers , 5 types, 253 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
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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: 2.92 Å3/Da / Density % sol: 57.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:0.1M NaHPO4, 0.1M MES, PEG 20K 12%, VAPOR DIFFUSION, SITTING DROP, temperature 277KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97918 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 12, 2011 / Details: Rh coated flat mirror |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 72527 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 48.7 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 4.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1Q92 Resolution: 1.6→29.039 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.35 / σ(F): 1.35 / Phase error: 16.57 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.229 Å2 / ksol: 0.382 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.6→29.039 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.7591 Å / Origin y: 20.2865 Å / Origin z: 18.8419 Å
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Refinement TLS group | Selection details: all |