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Yorodumi- PDB-6jqe: The structural basis of the beta-carbonic anhydrases CafD (wild t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jqe | |||||||||
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Title | The structural basis of the beta-carbonic anhydrases CafD (wild type) of the filamentous fungus Aspergillus fumigatus | |||||||||
Components | Carbonic anhydrase | |||||||||
Keywords | LYASE / beta-class carbonic anhydrase / Aspergillus fumigatus / CafD | |||||||||
Function / homology | Function and homology information cellular response to carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Neosartorya fumigata (mold) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 | 6jqe.cif.gz | 83.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jqe.ent.gz | 61.2 KB | Display | PDB format |
PDBx/mmJSON format | 6jqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/6jqe ftp://data.pdbj.org/pub/pdb/validation_reports/jq/6jqe | HTTPS FTP |
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-Related structure data
Related structure data | 6jqcC 6jqdC 6jor 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 9 - 179 / Label seq-ID: 1 - 171
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-Components
#1: Protein | Mass: 19129.621 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_8G06554 / Production host: Escherichia coli (E. coli) / References: UniProt: A4DA31, 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: 2.14 Å3/Da / Density % sol: 42.45 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 24-28% PEG3350, 200 mM MgCl2 and 100 mM HEPES pH 7.0-7.5 |
-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: Oct 24, 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: 1.9→50 Å / Num. obs: 22753 / % possible obs: 94 % / Redundancy: 2.6 % / Rpim(I) all: 0.077 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Num. unique obs: 2375 / Rpim(I) all: 0.455 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JOR 6jor Resolution: 1.9→46.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.622 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.174 / 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: 38.562 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→46.23 Å
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Refine LS restraints |
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