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- PDB-8dpc: Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae -
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Open data
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Basic information
Entry | Database: PDB / ID: 8dpc | ||||||
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Title | Crystal structure of carbonic anhydrase from Neisseria gonorrhoeae | ||||||
![]() | Carbonic anhydrase | ||||||
![]() | LYASE / Carbonic anhydrase / Neisseria gonorrhoeae | ||||||
Function / homology | ![]() regulation of pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / periplasmic space / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Marapaka, A.K. / Das, C. / Flaherty, D.P. / Yadav, R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Characterization of Thiadiazolesulfonamide Inhibitors Bound to Neisseria gonorrhoeae alpha-Carbonic Anhydrase. Authors: Marapaka, A.K. / Nocentini, A. / Youse, M.S. / An, W. / Holly, K.J. / Das, C. / Yadav, R. / Seleem, M.N. / Supuran, C.T. / Flaherty, D.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 190.3 KB | Display | ![]() |
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PDB format | ![]() | 149 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.7 MB | Display | ![]() |
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Full document | ![]() | 5.7 MB | Display | |
Data in XML | ![]() | 33.5 KB | Display | |
Data in CIF | ![]() | 46.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8dqfC ![]() 8dr2C ![]() 8drbC ![]() 8dyqC ![]() 1koqS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27315.727 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.15 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M NH4H2PO4, 2. 2.2 M (NH4)2SO4 / PH range: 6.0-7.4 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 46572 / % possible obs: 99.7 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.068 / Rrim(I) all: 0.173 / Χ2: 0.851 / Net I/σ(I): 5.1 / Num. measured all: 285624 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | ||||||
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Phasing MR | R rigid body: 0.562
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1KOQ Resolution: 2.41→44.12 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 8.057 / SU ML: 0.183 / SU R Cruickshank DPI: 0.3144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.242 / 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: 110.68 Å2 / Biso mean: 30.173 Å2 / Biso min: 2.96 Å2
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Refinement step | Cycle: final / Resolution: 2.41→44.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.41→2.468 Å / Rfactor Rfree error: 0
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