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- PDB-7qob: Human Carbonic Anhydrase I in complex with benzoselenoate -

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Basic information

Entry
Database: PDB / ID: 7qob
TitleHuman Carbonic Anhydrase I in complex with benzoselenoate
ComponentsCarbonic anhydrase 1
KeywordsLYASE / carbonic anhydrase I / inhibitor / metalloenzyme / benzoselenoate
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
benzoselenoate / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Bioorg.Chem. / Year: 2022
Title: Benzoselenoates: A novel class of carbonic anhydrase inhibitors.
Authors: Tanini, D. / Capperucci, A. / Locuoco, M. / Ferraroni, M. / Costantino, G. / Angeli, A. / Supuran, C.T.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,3136
Polymers57,8122
Non-polymers5014
Water4,324240
1
AAA: Carbonic anhydrase 1
hetero molecules


  • defined by author
  • 29.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,1573
Polymers28,9061
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Carbonic anhydrase 1
hetero molecules


  • defined by author
  • 29.2 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)29,1573
Polymers28,9061
Non-polymers2502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.080, 70.640, 121.630
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-E7I / benzoselenoate


Mass: 185.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6OSe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
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: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40.54 Å / Num. obs: 50254 / % possible obs: 99.8 % / Redundancy: 10.6 % / CC1/2: 0.78 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.061 / Rrim(I) all: 0.147 / Net I/σ(I): 8.8
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 10 % / Num. unique obs: 2944 / CC1/2: 0.798 / % possible all: 99.2

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Processing

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

1jv0


Resolution: 1.8→37.033 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.564 / SU ML: 0.128 / Cross valid method: NONE / ESU R: 0.141 / ESU R Free: 0.133
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2431 2375 4.739 %
Rwork0.205 47736 -
all0.207 --
obs-50111 99.482 %
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: 28.971 Å2
Baniso -1Baniso -2Baniso -3
1--1.459 Å20 Å20 Å2
2--3.847 Å2-0 Å2
3----2.389 Å2
Refinement stepCycle: LAST / Resolution: 1.8→37.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 20 240 4276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134164
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153768
X-RAY DIFFRACTIONr_angle_refined_deg1.71.6395669
X-RAY DIFFRACTIONr_angle_other_deg1.3061.5838726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7745514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43323.707205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25815662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9431514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024856
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02956
X-RAY DIFFRACTIONr_nbd_refined0.1930.2779
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23503
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21973
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21860
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1130.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0160.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.213
X-RAY DIFFRACTIONr_nbd_other0.2440.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.212
X-RAY DIFFRACTIONr_mcbond_it2.262.8932052
X-RAY DIFFRACTIONr_mcbond_other2.2442.8942049
X-RAY DIFFRACTIONr_mcangle_it3.1584.3352560
X-RAY DIFFRACTIONr_mcangle_other3.1584.3352561
X-RAY DIFFRACTIONr_scbond_it2.9223.1822112
X-RAY DIFFRACTIONr_scbond_other2.9213.1822113
X-RAY DIFFRACTIONr_scangle_it4.4664.6433107
X-RAY DIFFRACTIONr_scangle_other4.4664.6433108
X-RAY DIFFRACTIONr_lrange_it5.79134.1914573
X-RAY DIFFRACTIONr_lrange_other5.79534.1984571
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3941820.3943472X-RAY DIFFRACTION98.6235
1.847-1.8970.3791760.3353350X-RAY DIFFRACTION98.906
1.897-1.9520.3541620.3043287X-RAY DIFFRACTION98.8819
1.952-2.0120.3171710.283191X-RAY DIFFRACTION99.2619
2.012-2.0780.3031640.2473093X-RAY DIFFRACTION99.2685
2.078-2.1510.321440.2382996X-RAY DIFFRACTION99.3042
2.151-2.2320.2821420.2322945X-RAY DIFFRACTION99.5806
2.232-2.3230.241540.2052762X-RAY DIFFRACTION99.8288
2.323-2.4260.2591290.1972731X-RAY DIFFRACTION99.9301
2.426-2.5440.2871230.1962601X-RAY DIFFRACTION99.8168
2.544-2.6820.2521270.22466X-RAY DIFFRACTION99.846
2.682-2.8440.216980.1872368X-RAY DIFFRACTION99.7573
2.844-3.040.2821140.192198X-RAY DIFFRACTION99.7412
3.04-3.2830.2131050.1962061X-RAY DIFFRACTION99.8617
3.283-3.5950.221010.1911900X-RAY DIFFRACTION99.8503
3.595-4.0180.181720.1681741X-RAY DIFFRACTION99.8348
4.018-4.6360.191640.1591554X-RAY DIFFRACTION99.8149
4.636-5.670.189660.1721336X-RAY DIFFRACTION100
5.67-7.9840.22550.1741050X-RAY DIFFRACTION100
7.984-37.0330.178260.178634X-RAY DIFFRACTION98.8024

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