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- PDB-7ng1: Crystal structure of alpha Carbonic anhydrase from Schistoso ma m... -

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Basic information

Entry
Database: PDB / ID: 7ng1
TitleCrystal structure of alpha Carbonic anhydrase from Schistoso ma mansoni bound to 1-(4-iodophenyl)-3-[2-(4-sulfamoylphenyl)ethyl]selenourea
ComponentsCarbonic anhydrase
KeywordsLYASE
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / 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-TN8 / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.67 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
DepositionFeb 8, 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

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Assembly

Deposited unit
A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98711
Polymers75,8632
Non-polymers2,1249
Water8,395466
1
B: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,98711
Polymers75,8632
Non-polymers2,1249
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-y-1,-y-1,-z+1/31
Buried area3920 Å2
ΔGint-2 kcal/mol
Surface area22450 Å2
Unit cell
Length a, b, c (Å)103.279, 103.279, 132.799
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
#4: 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, 471 molecules

#2: Chemical ChemComp-TN8 / ~{N}'-(4-iodophenyl)-~{N}-[2-(4-sulfamoylphenyl)ethyl]carbamimidoselenoic acid


Mass: 508.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H16IN3O2SSe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#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.: 466 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
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: Sep 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.67→30 Å / Num. obs: 95367 / % possible obs: 100 % / Redundancy: 19.3 % / CC1/2: 1 / Rrim(I) all: 0.091 / Rsym value: 0.089 / Net I/σ(I): 23.77
Reflection shellResolution: 1.67→1.77 Å / Redundancy: 18.2 % / Mean I/σ(I) obs: 1.13 / Num. unique obs: 15234 / CC1/2: 0.566 / Rrim(I) all: 2.57 / Rsym value: 2.49 / % possible all: 99.8

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Processing

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

6qqm


Resolution: 1.67→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.17 / SU ML: 0.067 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 4725 5 %RANDOM
Rwork0.1777 ---
obs0.179 90629 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.4 Å2 / Biso mean: 33.796 Å2 / Biso min: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: final / Resolution: 1.67→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4478 0 110 466 5054
Biso mean--50.14 42.19 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124725
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6556437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.12822.109256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3315749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6911530
X-RAY DIFFRACTIONr_chiral_restr0.1030.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023752
LS refinement shellResolution: 1.67→1.712 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.404 337 -
Rwork0.393 6580 -
obs--99.48 %

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