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Yorodumi- PDB-4ao6: Native structure of a novel cold-adapted esterase from an Arctic ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ao6 | ||||||
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Title | Native structure of a novel cold-adapted esterase from an Arctic intertidal metagenomic library | ||||||
Components | ESTERASE | ||||||
Keywords | HYDROLASE / THERMO LABEL | ||||||
Function / homology | Alpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta Function and homology information | ||||||
Biological species | UNIDENTIFIED (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Fu, J. / Leiros, H.-K.S. / Pascale, D.d. / Johnson, K.A. / Blencke, H.M. / Landfald, B. | ||||||
Citation | Journal: Appl.Microbiol.Biotechnol. / Year: 2013 Title: Functional and Structural Studies of a Novel Cold-Adapted Esterase from an Arctic Intertidal Metagenomic Library. Authors: Fu, J. / Leiros, H.-K.S. / De Pascale, D. / Johnson, K.A. / Blencke, H.M. / Landfald, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ao6.cif.gz | 103.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ao6.ent.gz | 80.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ao6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ao6_validation.pdf.gz | 432.5 KB | Display | wwPDB validaton report |
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Full document | 4ao6_full_validation.pdf.gz | 437.8 KB | Display | |
Data in XML | 4ao6_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4ao6_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ao/4ao6 ftp://data.pdbj.org/pub/pdb/validation_reports/ao/4ao6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28294.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: A HIS-TAGGED CONSTRUCT / Source: (gene. exp.) UNIDENTIFIED (others) Description: FROM A METAGENOMIC LIBRARY FROM INTERTIDAL ZONE AT SVALBARD ARCHIPELAGO Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): M15 (PREP4) |
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#2: Water | ChemComp-HOH / |
Sequence details | RESIDUES MRGSHHHHHH |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 34.02 % / Description: NONE |
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Crystal grow | Details: 26-30% POLYETHYLENE GLYCOL (PEG) 3350, 3% GLYCEROL 0.1 M SODIUM MALONATE PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. obs: 28142 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 0 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.2 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: NONE Resolution: 1.6→25 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.172 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.094 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.423 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→25 Å
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Refine LS restraints |
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