+Open data
-Basic information
Entry | Database: PDB / ID: 3wj1 | ||||||
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Title | Crystal structure of SSHESTI | ||||||
Components | Carboxylesterase | ||||||
Keywords | HYDROLASE / ALPHA/BETA-HYDRORASE FOLD / CARBOXYLESTERASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sulfolobus shibatae (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Ohara, K. / Unno, H. / Oshima, Y. / Furukawa, K. / Fujino, N. / Hirooka, K. / Hemmi, H. / Takahashi, S. / Nishino, T. / Kusunoki, M. / Nakayama, T. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2014 Title: Structural insights into the low pH adaptation of a unique carboxylesterase from Ferroplasma: altering the pH optima of two carboxylesterases. Authors: Ohara, K. / Unno, H. / Oshima, Y. / Hosoya, M. / Fujino, N. / Hirooka, K. / Takahashi, S. / Yamashita, S. / Kusunoki, M. / Nakayama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wj1.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wj1.ent.gz | 58.1 KB | Display | PDB format |
PDBx/mmJSON format | 3wj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wj1 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wj1 | HTTPS FTP |
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-Related structure data
-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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-Components
#1: Protein | Mass: 33551.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus shibatae (archaea) / Gene: SshEstI / Plasmid: PTC99A / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5NU42, carboxylesterase |
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#2: Sugar | ChemComp-BOG / |
#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: 2.2 Å3/Da / Density % sol: 42.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 Details: 13% PEG MME 2000, 100MM TRIS-HCL, PH 7.00, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Feb 17, 2004 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→24.8 Å / Num. obs: 45391 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.08 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.6 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→24.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.036 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→24.8 Å
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Refine LS restraints |
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