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Yorodumi- PDB-6lac: The structural basis of the beta-carbonic anhydrase CafD (C39A mu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6lac | |||||||||
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Title | The structural basis of the beta-carbonic anhydrase CafD (C39A mutant) 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 / carbon utilization / 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: 1.3 Å | |||||||||
Authors | Jiin, 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: To be published Title: The structural analysis of non-catalytic zinc binding site in the minor beta-carbonic anhydrase CafD Authors: Jin, M.S. / Kim, S. / Kim, N.J. / Hong, S. / Kim, S. / Sung, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6lac.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6lac.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 6lac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lac_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6lac_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6lac_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 6lac_validation.cif.gz | 22.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/la/6lac ftp://data.pdbj.org/pub/pdb/validation_reports/la/6lac | HTTPS FTP |
-Related structure data
Related structure data | 6laiC 6jqeS 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
#1: Protein | Mass: 20197.867 Da / Num. of mol.: 2 / Mutation: C39A 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 / | Has ligand of interest | Y | |
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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: 2.15 Å3/Da / Density % sol: 42.68 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 28 % PEG3350, 200 mM MgCl2, 100 mM Tris-HCl pH 6.0-9.5 |
-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: Jun 1, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→50 Å / Num. obs: 75211 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rsym value: 0.02 / Net I/σ(I): 30.3 |
Reflection shell | Resolution: 1.3→1.35 Å / Num. unique obs: 7904 / Rsym value: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6JQE Resolution: 1.3→33.92 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.846 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 72.18 Å2 / Biso mean: 19.216 Å2 / Biso min: 8.1 Å2
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Refinement step | Cycle: final / Resolution: 1.3→33.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.333 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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