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

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


regulation of pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / 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-TBW / Carbonic anhydrase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 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

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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)111,92724
Polymers109,2634
Non-polymers2,66420
Water59433
1
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0787
Polymers27,3161
Non-polymers7626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9826
Polymers27,3161
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8865
Polymers27,3161
Non-polymers5704
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9826
Polymers27,3161
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.705, 121.890, 78.516
Angle α, β, γ (deg.)90.000, 116.590, 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-TBW / 3-phenyl-N-(5-sulfamoyl-1,3,4-thiadiazol-2-yl)propanamide


Mass: 312.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N4O3S2 / 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.: 12 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.58 %
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: 2.59→50 Å / Num. obs: 34669 / % possible obs: 94.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.076 / Rrim(I) all: 0.181 / Χ2: 1.03 / Net I/σ(I): 4.9 / Num. measured all: 176488
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.59-2.682.90.3327380.8640.1980.3880.50274.6
2.68-2.793.80.30730840.8920.1620.3490.60384.1
2.79-2.924.40.30234040.9040.1480.3380.74893
2.92-3.074.50.2735530.9140.1360.3040.84497.3
3.07-3.265.80.23536830.9560.1040.2571.06499.6
3.26-3.5160.19136520.9660.0850.211.2299.4
3.51-3.875.80.16236020.9750.0730.1781.12198.8
3.87-4.435.20.14235960.9660.070.1591.09596.8
4.43-5.585.70.13436440.9680.0630.1481.08698.4
5.58-1060.14137130.9750.0630.1561.26699.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.547
Highest resolutionLowest resolution
Rotation46.03 Å3.02 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: 2.59→46.03 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / SU B: 10.571 / SU ML: 0.227 / SU R Cruickshank DPI: 0.6691 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.669 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1687 4.9 %RANDOM
Rwork0.1905 ---
obs0.1936 32955 93.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.02 Å2 / Biso mean: 43.375 Å2 / Biso min: 11.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å2-0 Å2-0.04 Å2
2--0.05 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 2.59→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7006 0 144 33 7183
Biso mean--69.3 34.13 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0127349
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166443
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.66710011
X-RAY DIFFRACTIONr_angle_other_deg0.4881.56115076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0255884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.0281036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.146101174
X-RAY DIFFRACTIONr_chiral_restr0.0660.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028228
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021408
LS refinement shellResolution: 2.591→2.658 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 88 -
Rwork0.279 1724 -
all-1812 -
obs--67.54 %

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