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Yorodumi- PDB-8dqf: Crystal structure of Neisseria gonorrhoeae carbonic anhydrase wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dqf | ||||||
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Title | Crystal structure of Neisseria gonorrhoeae carbonic anhydrase with N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)cyclohexanecarboxamide | ||||||
Components | Carbonic anhydrase | ||||||
Keywords | LYASE / Carbonic anhydrase / Neisseria gonorrhoeae / Acetazolamide | ||||||
Function / homology | Function and homology information carbonic anhydrase / carbonate dehydratase activity / periplasmic space / zinc ion binding Similarity search - Function | ||||||
Biological species | Neisseria gonorrhoeae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å | ||||||
Authors | Marapaka, A.K. / Das, C. / Flaherty, D.P. / Yadav, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Med.Chem.Lett. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dqf.cif.gz | 190.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dqf.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 8dqf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dqf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8dqf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8dqf_validation.xml.gz | 34.8 KB | Display | |
Data in CIF | 8dqf_validation.cif.gz | 46.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqf ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqf | HTTPS FTP |
-Related structure data
Related structure data | 8dpcC 8dr2C 8drbC 8dyqC 1kopS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-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.) Neisseria gonorrhoeae (bacteria) / Gene: cah / Production host: Escherichia coli (E. coli) / References: UniProt: Q50940, carbonic anhydrase #2: Chemical | ChemComp-VGV / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-SO4 / #5: 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: 2.82 Å3/Da / Density % sol: 56.4 % |
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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 M (NH4)2SO4 / PH range: 6.4-7.4 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.78→50 Å / Num. obs: 29522 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.099 / Rrim(I) all: 0.21 / Χ2: 0.87 / Net I/σ(I): 4.2 / Num. measured all: 125611 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.549
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1KOP Resolution: 2.8→46.11 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.861 / SU B: 13.546 / SU ML: 0.265 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.367 / 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: 93.83 Å2 / Biso mean: 28.341 Å2 / Biso min: 6.16 Å2
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Refinement step | Cycle: final / Resolution: 2.8→46.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.868 Å / Rfactor Rfree error: 0
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