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Yorodumi- PDB-4uhe: Structural studies of a thermophilic esterase from Thermogutta te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uhe | ||||||
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Title | Structural studies of a thermophilic esterase from Thermogutta terrifontis (malate 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: 1.16 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 | 4uhe.cif.gz | 153.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uhe.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uhe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/4uhe ftp://data.pdbj.org/pub/pdb/validation_reports/uh/4uhe | HTTPS FTP |
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-Related structure data
Related structure data | 4uhcC 4uhdC 4uhfC 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 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-PGE / | ||||
#3: Chemical | #4: Chemical | ChemComp-MLT / | #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: 2.06 Å3/Da / Density % sol: 40.4 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / 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: 1.16→37.52 Å / Num. obs: 86054 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.16→1.19 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.2 / % possible all: 95.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2XUA Resolution: 1.16→37.52 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.101 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.032 / 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: 15.146 Å2
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Refinement step | Cycle: LAST / Resolution: 1.16→37.52 Å
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Refine LS restraints |
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