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- PDB-4e88: CRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, No... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4.0E+88 | ||||||
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Title | CRYSTAL STRUCTURE OF DE NOVO DESIGNED CYSTEINE ESTERASE ECH13, Northeast Structural Genomics Consortium Target OR51 | ||||||
![]() | DE NOVO DESIGNED CYSTEINE ESTERASE ECH13 | ||||||
![]() | HYDROLASE / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
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![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Kuzin, A. / Su, M. / Seetharaman, J. / Xiao, X. / Sahdev, S. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. / Montelione, G.T. ...Kuzin, A. / Su, M. / Seetharaman, J. / Xiao, X. / Sahdev, S. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
![]() | ![]() Title: Northeast Structural Genomics Consortium Target OR51 Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Xiao, X. / Sahdev, S. / Ciccosanti, C. / Richter, F. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.2 KB | Display | ![]() |
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PDB format | ![]() | 79.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.8 KB | Display | ![]() |
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Full document | ![]() | 437.4 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3u13S S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Details | dimer,54.06 kD,98.7% |
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Components
#1: Protein | Mass: 24209.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.53 % |
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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:100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M REMARK 280 ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M REMARK 280 NH4F, 20% PEG3350, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5) . RESERVOIR SOLUTION: 0.2M , VAPOR DIFFUSION, SITTING DROP, temperature 277KK |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
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 % / Biso Wilson estimate: 28.24 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 30.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3U13 Resolution: 2→23.091 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.866 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.488 Å2 / ksol: 0.322 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.78 Å2 / Biso mean: 33.286 Å2 / Biso min: 13.95 Å2
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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 | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Refinement TLS params. | Method: refined / Origin x: 10.9111 Å / Origin y: -31.222 Å / Origin z: -10.3695 Å
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Refinement TLS group |
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