+Open data
-Basic information
Entry | Database: PDB / ID: 5frd | ||||||
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Title | Structure of a thermophilic esterase | ||||||
Components | CARBOXYLESTERASE (EST-2) | ||||||
Keywords | HYDROLASE / ESTERASE | ||||||
Function / homology | Function and homology information Alpha/beta hydrolase family / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | ARCHAEOGLOBUS FULGIDUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Sayer, C. / Finnigan, W. / Isupov, M.N. / Levisson, M. / Kengen, S.W.M. / van der Oost, J. / Harmer, N. / Littlechild, J.A. | ||||||
Citation | Journal: Sci.Rep. / Year: 2016 Title: Structural and Biochemical Characterisation of Archaeoglobus Fulgidus Esterase Reveals a Bound Coa Molecule in the Vicinity of the Active Site. Authors: Sayer, C. / Finnigan, W. / Isupov, M.N. / Levisson, M. / Kengen, S.W. / Van Der Oost, J. / Harmer, N.J. / Littlechild, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5frd.cif.gz | 140.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5frd.ent.gz | 112.3 KB | Display | PDB format |
PDBx/mmJSON format | 5frd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/5frd ftp://data.pdbj.org/pub/pdb/validation_reports/fr/5frd | HTTPS FTP |
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-Related structure data
Related structure data | 1a8qS S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.85888, 0.49359, 0.13672), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29288.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: O28735, carboxylesterase |
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-Non-polymers , 6 types, 521 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-FLC / | #6: Chemical | ChemComp-PEG / | #7: 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: 2.31 Å3/Da / Density % sol: 46.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→70.3 Å / Num. obs: 102188 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.4→1.44 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 89.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1A8Q Resolution: 1.4→70.29 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.107 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.057 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.568 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→70.29 Å
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Refine LS restraints |
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