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Yorodumi- PDB-3u19: CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3u19 | ||||||
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Title | CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, 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 / coumarin | ||||||
Function / homology | 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 Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2 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: To be Published Title: CRYSTAL STRUCTURE OF ACYLENZYME INTERMEDIATE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51 Authors: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3u19.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u19.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3u19.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u19_validation.pdf.gz | 442 KB | Display | wwPDB validaton report |
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Full document | 3u19_full_validation.pdf.gz | 443.7 KB | Display | |
Data in XML | 3u19_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 3u19_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/3u19 ftp://data.pdbj.org/pub/pdb/validation_reports/u1/3u19 | HTTPS FTP |
-Related structure data
Related structure data | 1q92S S: Starting model for refinement |
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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
#1: Protein | Mass: 24326.154 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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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.58 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.2M NH4F, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 19, 2011 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 16356 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.9 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.1 / % possible all: 78.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: pdb entry 1Q92 Resolution: 2→23.091 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.49 / σ(F): 1.38 / Phase error: 20.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.074 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2→23.091 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: 10.9422 Å / Origin y: -31.2562 Å / Origin z: -10.3519 Å
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Refinement TLS group | Selection details: all |