+Open data
-Basic information
Entry | Database: PDB / ID: 6agq | ||||||
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Title | Acetyl xylan esterase from Paenibacillus sp. R4 | ||||||
Components | acetyl xylan esterase | ||||||
Keywords | HYDROLASE / Paenibacillus sp. / Acetyl esterase / acetyl xylan esterases | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Paenibacillus sp. R4 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Park, S. / Lee, C.W. / Lee, J.H. | ||||||
Citation | Journal: PLoS ONE / Year: 2018 Title: Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp. Authors: Park, S.H. / Yoo, W. / Lee, C.W. / Jeong, C.S. / Shin, S.C. / Kim, H.W. / Park, H. / Kim, K.K. / Kim, T.D. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6agq.cif.gz | 386.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6agq.ent.gz | 318 KB | Display | PDB format |
PDBx/mmJSON format | 6agq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/6agq ftp://data.pdbj.org/pub/pdb/validation_reports/ag/6agq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36177.918 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. R4 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSP2*PLUS #2: Chemical | ChemComp-ZN / #3: 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: 2.6 Å3/Da / Density % sol: 52.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.8 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 5.0 |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 121844 / % possible obs: 96.8 % / Redundancy: 3.7 % / Net I/σ(I): 27.2 |
Reflection shell | Resolution: 2.1→2.14 Å |
-Processing
Software |
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Refinement | Resolution: 2.1→49.39 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.481 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.204 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.78 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→49.39 Å
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Refine LS restraints |
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