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- PDB-7bm4: Crystal structure of alpha Carbonic anhydrase from Schistosoma ma... -

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Basic information

Entry
Database: PDB / ID: 7bm4
TitleCrystal structure of alpha Carbonic anhydrase from Schistosoma mansoni bound to 1-(4-fluorophenyl)-3-(4-sulphamoylphenyl)selenourea
ComponentsCarbonic anhydrase
KeywordsLYASE
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-U3N / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsFerraroni, M. / Angeli, A. / Supuran, C.T.
CitationJournal: J.Med.Chem. / Year: 2021
Title: Structural Insights into Schistosoma mansoni Carbonic Anhydrase (SmCA) Inhibition by Selenoureido-Substituted Benzenesulfonamides.
Authors: Angeli, A. / Ferraroni, M. / Da'dara, A.A. / Selleri, S. / Pinteala, M. / Carta, F. / Skelly, P.J. / Supuran, C.T.
History
DepositionJan 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,80712
Polymers75,8632
Non-polymers1,94410
Water11,241624
1
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9046
Polymers37,9321
Non-polymers9725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9046
Polymers37,9321
Non-polymers9725
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.896, 102.896, 132.225
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, 6 molecules AB

#1: Protein Carbonic anhydrase


Mass: 37931.516 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.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
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, 630 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-U3N / 1-(4-fluorophenyl)-3-(4-sulfamoylphenyl)selenourea


Mass: 372.277 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12FN3O2SSe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 20% PEG 3350, 0.2 M POTASSIUM NITRATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2019
RadiationMonochromator: Double Crystal Manochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 106677 / % possible obs: 99.7 % / Redundancy: 19.01 % / Biso Wilson estimate: 29.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.066 / Rsym value: 0.064 / Χ2: 0.895 / Net I/σ(I): 32.23 / Num. measured all: 2036307
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) allRsym value% possible all
1.6-1.718.11.1312.8730453533398168380.8681.1961.16398.5
1.7-1.819.3920.6263.7929492431450314030.9140.66399.9
1.81-1.9610.0620.3237.4629397129231292150.980.34199.9
1.96-2.159.8270.17713.226488026958269530.9930.187100
2.15-2.410.2510.10621.924945724334243340.9970.112100
2.4-2.7710.3180.06335.7322108221427214270.9990.067100
2.77-3.3910.3250.04153.9118720918132181320.9990.043100
3.39-4.7810.1280.02681.12142386140581405810.027100
4.78-3010.0130.02288.33778597793777610.02499.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6QQM

6qqm


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.1776 / WRfactor Rwork: 0.1533 / FOM work R set: 0.8765 / SU B: 1.402 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0687 / SU Rfree: 0.0717 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 5286 5 %RANDOM
Rwork0.1657 ---
obs0.167 101338 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.84 Å2 / Biso mean: 27.654 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 112 624 5204
Biso mean--41.39 39.85 -
Num. residues----552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0124723
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.6566438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0395558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.58722.14257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63415746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0531530
X-RAY DIFFRACTIONr_chiral_restr0.1190.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023765
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 371 -
Rwork0.284 7230 -
all-7601 -
obs--97.4 %

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