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- PDB-7plf: Human Carbonic Anhydrase I in complex with clorsulon -

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Basic information

Entry
Database: PDB / ID: 7plf
TitleHuman Carbonic Anhydrase I in complex with clorsulon
ComponentsCarbonic anhydrase 1
KeywordsLYASE / carbonic anhydrase I / clorsulon / inhibitor / sulfonamide / metalloenzyme
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.461 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
DepositionAug 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Carbonic anhydrase 1
BBB: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7056
Polymers57,8122
Non-polymers8924
Water7,602422
1
AAA: Carbonic anhydrase 1
hetero molecules


  • defined by author
  • 29.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,3523
Polymers28,9061
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Carbonic anhydrase 1
hetero molecules


  • defined by author
  • 29.4 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,3523
Polymers28,9061
Non-polymers4462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.270, 71.340, 121.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00915, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9718 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.46→46.92 Å / Num. obs: 94318 / % possible obs: 100 % / Redundancy: 12.46 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.065 / Net I/σ(I): 20
Reflection shellResolution: 1.46→1.5 Å / Redundancy: 12.63 % / Rmerge(I) obs: 1.191 / Num. unique obs: 6929 / CC1/2: 0.838 / Rrim(I) all: 1.241 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JV0

1jv0


Resolution: 1.461→46.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.365 / SU ML: 0.051 / Cross valid method: NONE / ESU R: 0.066 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.205 4682 4.964 %
Rwork0.1772 89636 -
all0.179 --
obs-94318 99.974 %
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: 22.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.506 Å20 Å20 Å2
2--1.446 Å2-0 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.461→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4039 0 42 422 4503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134224
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173800
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.6395769
X-RAY DIFFRACTIONr_angle_other_deg1.481.5848805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82323.816207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97215669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1491514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02969
X-RAY DIFFRACTIONr_nbd_refined0.2060.2775
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1860.23661
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22005
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21993
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2290
X-RAY DIFFRACTIONr_metal_ion_refined0.0740.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1920.28
X-RAY DIFFRACTIONr_nbd_other0.1760.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1920.220
X-RAY DIFFRACTIONr_mcbond_it1.9142.1162070
X-RAY DIFFRACTIONr_mcbond_other1.9062.1162069
X-RAY DIFFRACTIONr_mcangle_it2.593.1762589
X-RAY DIFFRACTIONr_mcangle_other2.5843.1752588
X-RAY DIFFRACTIONr_scbond_it3.3892.4182154
X-RAY DIFFRACTIONr_scbond_other3.2972.4062149
X-RAY DIFFRACTIONr_scangle_it4.9873.5083174
X-RAY DIFFRACTIONr_scangle_other4.8633.4943169
X-RAY DIFFRACTIONr_lrange_it5.69925.7594660
X-RAY DIFFRACTIONr_lrange_other5.68125.7654660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.461-1.4990.2763710.2736552X-RAY DIFFRACTION99.9134
1.499-1.540.2773130.2456385X-RAY DIFFRACTION99.9702
1.54-1.5850.2673420.2236202X-RAY DIFFRACTION99.9694
1.585-1.6330.2282960.2186052X-RAY DIFFRACTION99.9843
1.633-1.6870.2473020.2025867X-RAY DIFFRACTION99.9838
1.687-1.7460.2352940.1925667X-RAY DIFFRACTION99.9832
1.746-1.8120.22940.185490X-RAY DIFFRACTION99.9827
1.812-1.8860.2042560.1775280X-RAY DIFFRACTION99.9639
1.886-1.9690.2142710.1775061X-RAY DIFFRACTION99.9812
1.969-2.0660.2162420.184870X-RAY DIFFRACTION99.9804
2.066-2.1770.2132410.1814605X-RAY DIFFRACTION100
2.177-2.3090.2012210.1744435X-RAY DIFFRACTION99.9785
2.309-2.4680.1972200.1694109X-RAY DIFFRACTION100
2.468-2.6660.2262120.1743832X-RAY DIFFRACTION100
2.666-2.9190.21850.173570X-RAY DIFFRACTION100
2.919-3.2630.2111920.1753235X-RAY DIFFRACTION99.9708
3.263-3.7660.1841480.1722869X-RAY DIFFRACTION100
3.766-4.6080.1761200.1452461X-RAY DIFFRACTION100
4.608-6.4990.1691140.1611941X-RAY DIFFRACTION99.9514
6.499-46.9570.209480.1871154X-RAY DIFFRACTION99.6683

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