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- PDB-7pri: Carbonic Anhydrase from Schistosoma Mansoni in complex with clorsulon -

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Basic information

Entry
Database: PDB / ID: 7pri
TitleCarbonic Anhydrase from Schistosoma Mansoni in complex with clorsulon
ComponentsCarbonic anhydrase
KeywordsLYASE / inhibitor / sulfonamide / schistosoma / schistosomiasis
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / zinc ion binding / plasma membrane
Similarity search - Function
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-7TI / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.679 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Inhibition of Schistosoma mansoni carbonic anhydrase by the antiparasitic drug clorsulon: X-ray crystallographic and in vitro studies.
Authors: Ferraroni, M. / Angeli, A. / Carradori, S. / Supuran, C.T.
History
DepositionSep 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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
AAA: Carbonic anhydrase
BBB: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,31012
Polymers64,2202
Non-polymers2,09010
Water6,738374
1
AAA: Carbonic anhydrase
hetero molecules


  • defined by author&software
  • 33 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)32,9995
Polymers32,1101
Non-polymers8884
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
BBB: Carbonic anhydrase
hetero molecules


  • defined by author&software
  • 33.3 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)33,3127
Polymers32,1101
Non-polymers1,2026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.800, 103.800, 132.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 7 molecules AAABBB

#1: Protein Carbonic anhydrase


Mass: 32110.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: A0A3Q0KSG2, carbonic anhydrase
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 379 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-7TI / 4-azanyl-6-[1,2,2-tris(chloranyl)ethenyl]benzene-1,3-disulfonamide / clorsulon


Mass: 380.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H8Cl3N3O4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.22 Å3/Da / Density % sol: 61.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG 6000, 0.1 M citrate pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9719 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9719 Å / Relative weight: 1
ReflectionResolution: 1.68→89.9 Å / Num. obs: 94460 / % possible obs: 99.7 % / Redundancy: 17.26 % / CC1/2: 1 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.099 / Net I/σ(I): 27.43
Reflection shellResolution: 1.68→1.72 Å / Redundancy: 8.93 % / Rmerge(I) obs: 1.18 / Num. unique obs: 6740 / CC1/2: 0.706 / Rrim(I) all: 1 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QQM

6qqm


Resolution: 1.679→89.893 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.191 / WRfactor Rwork: 0.163 / SU B: 1.562 / SU ML: 0.051 / Average fsc free: 0.9429 / Average fsc work: 0.9495 / Cross valid method: NONE / ESU R: 0.076 / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1951 4543 4.81 %
Rwork0.1669 89907 -
all0.168 --
obs-94450 99.685 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20.013 Å20 Å2
2--0.025 Å2-0 Å2
3----0.082 Å2
Refinement stepCycle: LAST / Resolution: 1.679→89.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 118 374 4986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134749
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174314
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.6716480
X-RAY DIFFRACTIONr_angle_other_deg1.4281.5959924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5445556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77121.985262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.69115758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.111532
X-RAY DIFFRACTIONr_chiral_restr0.0830.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021168
X-RAY DIFFRACTIONr_nbd_refined0.2070.2826
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24183
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22341
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.22184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0650.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0770.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.28
X-RAY DIFFRACTIONr_nbd_other0.2050.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.217
X-RAY DIFFRACTIONr_mcbond_it2.1722.1612218
X-RAY DIFFRACTIONr_mcbond_other2.1582.1582216
X-RAY DIFFRACTIONr_mcangle_it2.9983.2312772
X-RAY DIFFRACTIONr_mcangle_other2.9923.232770
X-RAY DIFFRACTIONr_scbond_it3.472.552531
X-RAY DIFFRACTIONr_scbond_other3.372.5412526
X-RAY DIFFRACTIONr_scangle_it5.2333.73706
X-RAY DIFFRACTIONr_scangle_other5.0893.693701
X-RAY DIFFRACTIONr_lrange_it6.77426.5245237
X-RAY DIFFRACTIONr_lrange_other6.64126.5015234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.679-1.7230.2643470.25963720.2669260.8720.87497.01130.244
1.723-1.770.2523160.21563630.21767500.9120.91698.94820.194
1.77-1.8210.223140.18962830.1966020.9270.93699.92430.164
1.821-1.8770.1922680.17961100.17963780.9460.9481000.152
1.877-1.9390.2042880.17559120.17762000.9420.9491000.147
1.939-2.0070.1953340.16456910.16660250.9550.961000.14
2.007-2.0830.1973080.17754790.17857870.950.9541000.152
2.083-2.1680.212640.16753240.16955880.9450.9581000.146
2.168-2.2640.1912410.16651130.16853540.9520.9591000.146
2.264-2.3740.1942320.15649020.15751340.9580.9661000.14
2.374-2.5030.2032480.15746380.15948860.9510.9631000.145
2.503-2.6540.1732360.15744090.15846450.9640.9641000.148
2.654-2.8380.1882370.16141180.16243550.9540.9611000.155
2.838-3.0650.1981810.16838920.16940730.9530.9631000.166
3.065-3.3570.1941700.17635960.17737660.9590.9611000.18
3.357-3.7520.1831560.16332580.16434140.9640.971000.171
3.752-4.3310.1521630.13628770.13630400.9740.9791000.151
4.331-5.3020.1441040.13724750.13725790.9830.9831000.159
5.302-7.4850.242900.18419550.18620450.9610.971000.208
7.485-89.8930.338460.20711400.21211890.8990.94699.74770.237

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