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Yorodumi- PDB-4uhf: Structural studies of a thermophilic esterase from Thermogutta te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uhf | ||||||
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Title | Structural studies of a thermophilic esterase from Thermogutta terrifontis (L37A mutant with butyrate bound) | ||||||
Components | ESTERASE | ||||||
Keywords | HYDROLASE / ALPHA BETA HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PLANCTOMYCETES BACTERIUM R1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å | ||||||
Authors | Sayer, C. / Isupov, M.N. / Bonch-Osmolovskaya, E. / Littlechild, J.A. | ||||||
Citation | Journal: FEBS J. / Year: 2015 Title: Structural Studies of a Thermophilic Esterase from a New Planctomycetes Species, Thermogutta Terrifontis. Authors: Sayer, C. / Isupov, M.N. / Bonch-Osmolovskaya, E. / 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 | 4uhf.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uhf.ent.gz | 124 KB | Display | PDB format |
PDBx/mmJSON format | 4uhf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/4uhf ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uhf | HTTPS FTP |
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-Related structure data
Related structure data | 4uhcC 4uhdC 4uheC 4uhhC 2xuaS C: citing same article (ref.) 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 31172.900 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLANCTOMYCETES BACTERIUM R1 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ARCTICEXPRESS RIL / References: UniProt: A0A0M3KKY6*PLUS, carboxylesterase | ||||
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#2: Chemical | ChemComp-CAD / | ||||
#3: Chemical | #4: Chemical | ChemComp-PGE / | #5: 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: 2.04 Å3/Da / Density % sol: 39.2 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→37.97 Å / Num. obs: 107910 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.08→1.11 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XUA Resolution: 1.08→37.97 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.819 / SU ML: 0.017 / Cross valid method: THROUGHOUT / ESU R: 0.025 / ESU R Free: 0.025 / 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: 16.721 Å2
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Refinement step | Cycle: LAST / Resolution: 1.08→37.97 Å
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Refine LS restraints |
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