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- PDB-7o2s: Crystal structure of a tetrameric form of Carbonic anhydrase from... -

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Basic information

Entry
Database: PDB / ID: 7o2s
TitleCrystal structure of a tetrameric form of Carbonic anhydrase from Schistosoma mansoni
ComponentsCarbonic anhydrase
KeywordsLYASE / complex / inhibitor
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
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsFerraroni, M. / Angeli, A.
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
DepositionMar 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 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 1.3Nov 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9709
Polymers37,9321
Non-polymers1,0388
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-159 kcal/mol
Surface area12680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.814, 77.814, 138.248
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Carbonic anhydrase


Mass: 37931.516 Da / Num. of mol.: 1
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
#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.: 1
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.: 1 / 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
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 20% PEG 3000, 0.2 M zinc acetate, 0.1 M Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.039867 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationMonochromator: Si (111) Double Crystal Manochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.039867 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. obs: 20050 / % possible obs: 99.5 % / Redundancy: 8.257 % / Biso Wilson estimate: 65.934 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.157 / Rrim(I) all: 0.168 / Χ2: 0.858 / Net I/σ(I): 6.68 / Num. measured all: 165561 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.28-2.348.1952.6120.711408145613920.172.78695.6
2.34-2.48.5642.0430.9412135141814170.3352.17399.9
2.4-2.478.3061.7271.1411396137413720.3861.84299.9
2.47-2.557.9951.3011.4710729134313420.4961.39299.9
2.55-2.638.681.0291.9911353130913080.6941.09599.9
2.63-2.728.6530.7912.5610903126012600.7490.843100
2.72-2.838.5170.643.1910485123112310.8460.683100
2.83-2.948.3560.4564.319860118211800.9050.48799.8
2.94-3.077.8080.3555.218792112811260.9230.38299.8
3.07-3.228.3760.2497.189222110111010.9620.267100
3.22-3.48.5670.1889.168850103310330.9780.201100
3.4-3.68.4750.15211.3183149819810.980.162100
3.6-3.858.220.1312.7777109409380.9860.13999.8
3.85-4.167.8260.11613.7567468718620.9880.12499
4.16-4.568.5720.10915.5269528118110.9920.116100
4.56-5.098.2620.10315.8760487327320.9930.11100
5.09-5.887.6290.10715.5250736706650.990.11499.3
5.88-7.27.8120.1115.7944375695680.9910.11799.8
7.2-10.197.4450.10416.3233654534520.9890.11299.8
10.19-306.3910.09915.3717832892790.9920.10896.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.392
Highest resolutionLowest resolution
Rotation43.05 Å2.98 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4pxx

4pxx


Resolution: 2.28→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2594 / WRfactor Rwork: 0.2102 / FOM work R set: 0.7134 / SU B: 9.621 / SU ML: 0.206 / SU R Cruickshank DPI: 0.2305 / SU Rfree: 0.2053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 1002 5 %RANDOM
Rwork0.2051 ---
obs0.2076 19027 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 146.54 Å2 / Biso mean: 65.704 Å2 / Biso min: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-0 Å2
2--0.4 Å2-0 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 2.28→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2218 0 47 36 2301
Biso mean--98.33 62.9 -
Num. residues----276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122323
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6673170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0675275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09122.177124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40815362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.811514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021794
LS refinement shellResolution: 2.28→2.337 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.444 69 -
Rwork0.391 1315 -
obs--95.65 %

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