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- PDB-8dr2: Crystal structure of Neisseria gonorrhoeae carbonic anhydrase wit... -

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Entry
Database: PDB / ID: 8dr2
TitleCrystal structure of Neisseria gonorrhoeae carbonic anhydrase with 2-cyclohexyl-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)acetamide
ComponentsCarbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / Neisseria gonorrhoeae / Acetazolamide
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / periplasmic space / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
Chem-TE3 / Carbonic anhydrase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.81 Å
AuthorsMarapaka, A.K. / Das, C. / Flaherty, D.P. / Yadav, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148523 United States
CitationJournal: 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
DepositionJul 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase
C: Carbonic anhydrase
E: Carbonic anhydrase
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,70322
Polymers109,2634
Non-polymers2,44018
Water32418
1
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8785
Polymers27,3161
Non-polymers5624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8785
Polymers27,3161
Non-polymers5624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9746
Polymers27,3161
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9746
Polymers27,3161
Non-polymers6585
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.673, 120.583, 80.423
Angle α, β, γ (deg.)90.000, 116.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carbonic anhydrase / Carbonate dehydratase


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-TE3 / 2-cyclohexyl-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)acetamide


Mass: 304.389 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.81→50 Å / Num. obs: 27473 / % possible obs: 91.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.079 / Rrim(I) all: 0.174 / Χ2: 0.737 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.82-2.922.50.34523050.7710.230.4170.3977.2
2.92-3.042.90.326250.8670.1880.3570.45187.4
3.04-3.183.90.2628130.9160.1390.2970.50794.6
3.18-3.344.60.22328420.9520.1110.250.56694.8
3.34-3.554.90.18928430.9590.0920.2110.62595.3
3.55-3.834.70.17328380.9680.0860.1940.70594
3.83-4.214.70.14227440.970.0720.160.69992.3
4.21-4.824.30.11726770.9690.0630.1340.8588.9
4.82-6.075.30.1128830.9790.0540.1240.82895.5
6.07-104.90.11829030.9740.0610.1341.26695.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.542
Highest resolutionLowest resolution
Rotation46.2 Å2.98 Å

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Processing

Software
NameVersionClassification
DENZO722data reduction
SCALEPACKdata scaling
MOLREP11.9.02phasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KOP

1kop


Resolution: 2.81→46.2 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.846 / SU B: 15.645 / SU ML: 0.294 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 1321 4.8 %RANDOM
Rwork0.192 ---
obs0.1956 26132 91.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 165.39 Å2 / Biso mean: 37.229 Å2 / Biso min: 4.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.01 Å2
2---0.05 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 2.81→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 130 18 7130
Biso mean--51.15 20.24 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0127313
X-RAY DIFFRACTIONr_bond_other_d0.0020.0166437
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.6669967
X-RAY DIFFRACTIONr_angle_other_deg0.4771.56415064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7145884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.511036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.736101160
X-RAY DIFFRACTIONr_chiral_restr0.0590.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021384
LS refinement shellResolution: 2.814→2.887 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 78 -
Rwork0.311 1488 -
all-1566 -
obs--70.22 %

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