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

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Basic information

Entry
Database: PDB / ID: 7nex
TitleCrystal structure of alpha Carbonic anhydrase from Schistosoma mansoni bound to 1-(4-fluorophenyl)-3-(4-sulfamoylph enyl)thiourea
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-8JS / Carbonic anhydrase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 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 5, 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

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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)78,45212
Polymers75,8632
Non-polymers2,58910
Water5,044280
1
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0606
Polymers37,9321
Non-polymers1,1285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3926
Polymers37,9321
Non-polymers1,4615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.800, 103.800, 133.030
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 , 1 types, 2 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

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Sugars , 2 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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.: 2 / 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, 285 molecules

#4: 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: Chemical ChemComp-8JS / 4-{[(4-fluorophenyl)carbamothioyl]amino}benzene-1-sulfonamide


Mass: 325.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12FN3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.8 Å3/Da / Density % sol: 56.02 %
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: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.81→30 Å / Num. obs: 75050 / % possible obs: 98.5 % / Redundancy: 19.2 % / Biso Wilson estimate: 40.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.062 / Rsym value: 0.06 / Χ2: 0.813 / Net I/σ(I): 33.1 / Num. measured all: 2056854
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsRrim(I) all% possible allMean I/σ(I) obsCC1/2Rmerge(I) obsRsym value
1.37-1.452.4058343209.28529.7
1.45-1.555.2071820012.74168.70.1
1.55-1.678.646229566.0993.20.3
1.67-1.8315.672226822.27499.91.220.627
1.83-2.0519.211200740.79397.24.320.9580.772
2.05-2.3619.174176140.29496.512.160.9920.286
2.36-2.919.841154720.09610034.310.9990.094
2.9-4.0919.403120770.03710078.8910.036
4.09-3017.93368800.02799.9109.0610.026
1.81-1.9218.8117851.32696.72.390.9211.29

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Processing

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

6qqm


Resolution: 1.81→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.775 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 3668 5 %RANDOM
Rwork0.1953 ---
obs0.1969 69990 96.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.82 Å2 / Biso mean: 36.727 Å2 / Biso min: 20.84 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4468 0 162 280 4910
Biso mean--68.34 39.27 -
Num. residues----554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124866
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.6766662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1915583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.74122.045264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.13315755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2131531
X-RAY DIFFRACTIONr_chiral_restr0.1230.2664
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023899
LS refinement shellResolution: 1.81→1.856 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.281 284 -
Rwork0.252 5290 -
obs--99.87 %

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