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Yorodumi- PDB-6iym: Fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguoba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iym | ||||||
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Title | Fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum | ||||||
Components | 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase | ||||||
Keywords | HYDROLASE / fumarylacetoacetate hydrolase / Exiguobacterium antarctica | ||||||
Function / homology | Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / catalytic activity / Alpha-Beta Complex / Alpha Beta / 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase Function and homology information | ||||||
Biological species | Exiguobacterium antarcticum B7 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Lee, J.H. / Lee, C.W. | ||||||
Citation | Journal: Biochem. Biophys. Res. Commun. / Year: 2019 Title: Structural and functional analysis of a dimeric fumarylacetoacetate hydrolase (EaFAH) from psychrophilic Exiguobacterium antarcticum. Authors: Yoo, W. / Lee, C.W. / Kim, B.Y. / Huong Luu Le, L.T. / Park, S.H. / Kim, H.W. / Shin, S.C. / Kim, K.K. / Lee, J.H. / Kim, T.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iym.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iym.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 6iym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iym_validation.pdf.gz | 437.7 KB | Display | wwPDB validaton report |
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Full document | 6iym_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 6iym_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 6iym_validation.cif.gz | 30.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iym ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iym | HTTPS FTP |
-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: 31595.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Exiguobacterium antarcticum B7 (bacteria) Strain: B7 / Gene: Eab7_1027 / Production host: Escherichia coli (E. coli) / References: UniProt: K0A9N9 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | This sequence is based on GenBank WP_026831132. | |
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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: 2.22 Å3/Da / Density % sol: 44.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2M magnesium chloride, 0.1M Tris-HCl pH 8.5, 20% (w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 200 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 30928 / % possible obs: 99.1 % / Redundancy: 6.4 % / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.1→2.16 Å |
-Processing
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Refinement | Resolution: 2.1→47.91 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.281 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.224 / 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: 52.744 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→47.91 Å
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