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Yorodumi- PDB-5ao9: The structure of a novel thermophilic esterase from the Planctomy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ao9 | ||||||
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Title | The structure of a novel thermophilic esterase from the Planctomycetes species, Thermogutta terrifontis, Est2-native | ||||||
Components | ESTERASE | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | THERMOGUTTA TERRIFONTIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Sayer, C. / Szabo, Z. / Isupov, M.N. / Ingham, C. / Littlechild, J.A. | ||||||
Citation | Journal: Front.Microbiol. / Year: 2015 Title: The Structure of a Novel Thermophilic Esterase from the Planctomycetes Species, Thermogutta Terrifontis Reveals an Open Active Site due to a Minimal 'CAP' Domain. Authors: Sayer, C. / Szabo, Z. / Isupov, M.N. / Ingham, C. / 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 | 5ao9.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ao9.ent.gz | 61.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ao9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/5ao9 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/5ao9 | HTTPS FTP |
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-Related structure data
Related structure data | 5aoaC 5aobC 5aocC 1evqS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 31557.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) THERMOGUTTA TERRIFONTIS (bacteria) / Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0X1KHD1*PLUS, carboxylesterase |
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-Non-polymers , 7 types, 224 molecules
#2: Chemical | ChemComp-EPE / | ||||||||
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#3: Chemical | ChemComp-PE8 / | ||||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 |
Detector | Type: DECTRIS PIXEL / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91741 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→47.8 Å / Num. obs: 46778 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.58→1.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.87 / 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 1EVQ Resolution: 1.58→47.83 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.431 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / 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: 29.383 Å2
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Refinement step | Cycle: LAST / Resolution: 1.58→47.83 Å
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Refine LS restraints |
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