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Yorodumi- PDB-6jqc: The structural basis of the beta-carbonic anhydrase CafC (wild ty... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jqc | |||||||||
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Title | The structural basis of the beta-carbonic anhydrase CafC (wild type) of the filamentous fungus Aspergillus fumigatus | |||||||||
Components | Carbonic anhydrase | |||||||||
Keywords | LYASE / CafC / beta-class carbonic anhydrase / Aspergillus fumigatus | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Neosartorya fumigata (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Jin, M.S. / Kim, S. / Kim, N.J. / Hong, S. / Kim, S. / Sung, J. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2019 Title: The structural basis of the low catalytic activities of the two minor beta-carbonic anhydrases of the filamentous fungus Aspergillus fumigatus. Authors: Kim, S. / Kim, N.J. / Hong, S. / Kim, S. / Sung, J. / Jin, M.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jqc.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jqc.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 6jqc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/6jqc ftp://data.pdbj.org/pub/pdb/validation_reports/jq/6jqc | HTTPS FTP |
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-Related structure data
Related structure data | 6jqdC 6jqeC 1g5cS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 164 / Label seq-ID: 1 - 164
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-Components
#1: Protein | Mass: 18149.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold) Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_4G09420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WPJ0, carbonic anhydrase #2: Chemical | #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: 2.06 Å3/Da / Density % sol: 40.35 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1-11% PEG2000 and 100 mM sodium acetate pH 4.5-5.5 |
-Data collection
Diffraction | Mean temperature: 77 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 17, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 24771 / % possible obs: 91.5 % / Redundancy: 2.6 % / Rpim(I) all: 0.069 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.8→1.86 Å / Num. unique obs: 2463 / Rpim(I) all: 0.311 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1G5C Resolution: 1.8→40.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.034 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.161 / 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: 23.668 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→40.07 Å
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Refine LS restraints |
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