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- PDB-9ep2: Crystal structure of the complex of human carbonic anhydrase I wi... -

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Basic information

Entry
Database: PDB / ID: 9ep2
TitleCrystal structure of the complex of human carbonic anhydrase I with 4-sulfamoylphenyl 3-(p-tolylthio)propanoate
ComponentsCarbonic anhydrase 1
KeywordsLYASE / carbonic anhydrase / sulfonamide / inhibitor / 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 / extracellular exosome / zinc ion binding / cytosol / cytoplasm
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
: / ACETATE ION / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of the complex of human carbonic anhydrase I with 4-sulfamoylphenyl 3-(p-tolylthio)propanoate
Authors: Angeli, A. / Ferraroni, M.
History
DepositionMar 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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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)58,7648
Polymers57,8122
Non-polymers9526
Water7,963442
1
AAA: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4415
Polymers28,9061
Non-polymers5354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3233
Polymers28,9061
Non-polymers4172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.640, 70.900, 121.250
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1H6C / (4-sulfamoylphenyl) 3-(4-methylphenyl)sulfanylpropanoate / 4-sulfamoylphenyl 3-(p-tolylthio)propanoate


Mass: 351.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H17NO4S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 47.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 28-31% PEG4000, 0.2 M sodium acetate, 0.1 M Tris pH 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: May 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.47→61.2 Å / Num. obs: 92188 / % possible obs: 99.9 % / Redundancy: 12.43 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.078 / Net I/σ(I): 17.35
Reflection shellResolution: 1.47→1.51 Å / Redundancy: 12.29 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 6734 / CC1/2: 0.826 / Rrim(I) all: 1.325 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→61.2 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / SU B: 7.099 / SU ML: 0.103 / Cross valid method: NONE / ESU R: 0.076 / ESU R Free: 0.072
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2086 4708 5.107 %
Rwork0.1603 87480 -
all0.163 --
obs-92188 99.891 %
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: 26.347 Å2
Baniso -1Baniso -2Baniso -3
1--1.616 Å20 Å20 Å2
2--6.008 Å2-0 Å2
3----4.391 Å2
Refinement stepCycle: LAST / Resolution: 1.47→61.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4042 0 56 442 4540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0134284
X-RAY DIFFRACTIONr_bond_other_d0.0040.0173765
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.6355846
X-RAY DIFFRACTIONr_angle_other_deg1.51.5868815
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17523.619210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77215679
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4461515
X-RAY DIFFRACTIONr_chiral_restr0.0930.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024924
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02881
X-RAY DIFFRACTIONr_nbd_refined0.2080.2842
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.23615
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22039
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21784
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2361
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.080.23
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.219
X-RAY DIFFRACTIONr_nbd_other0.2140.283
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.225
X-RAY DIFFRACTIONr_mcbond_it3.5822.5342091
X-RAY DIFFRACTIONr_mcbond_other3.582.5332090
X-RAY DIFFRACTIONr_mcangle_it3.9033.8182614
X-RAY DIFFRACTIONr_mcangle_other3.9033.8182615
X-RAY DIFFRACTIONr_scbond_it5.1172.9052193
X-RAY DIFFRACTIONr_scbond_other5.1162.9052194
X-RAY DIFFRACTIONr_scangle_it5.6714.2053221
X-RAY DIFFRACTIONr_scangle_other5.674.2053222
X-RAY DIFFRACTIONr_lrange_it5.56631.3054875
X-RAY DIFFRACTIONr_lrange_other5.56631.3054876
X-RAY DIFFRACTIONr_rigid_bond_restr12.79638049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.471-1.5090.3323320.3026382X-RAY DIFFRACTION99.6438
1.509-1.5510.2793240.276289X-RAY DIFFRACTION100
1.551-1.5960.2893080.2456064X-RAY DIFFRACTION99.9843
1.596-1.6450.2833400.2275886X-RAY DIFFRACTION99.9198
1.645-1.6990.2563080.215705X-RAY DIFFRACTION100
1.699-1.7580.2423100.2045528X-RAY DIFFRACTION99.9658
1.758-1.8250.2242860.185346X-RAY DIFFRACTION99.9468
1.825-1.8990.2462990.185159X-RAY DIFFRACTION99.9268
1.899-1.9830.2252620.1624910X-RAY DIFFRACTION99.8648
1.983-2.080.2262550.1574742X-RAY DIFFRACTION99.8801
2.08-2.1920.2142500.154507X-RAY DIFFRACTION99.958
2.192-2.3250.2221940.1464328X-RAY DIFFRACTION99.9116
2.325-2.4850.2022000.144053X-RAY DIFFRACTION99.9295
2.485-2.6840.2162120.1413743X-RAY DIFFRACTION99.9242
2.684-2.940.1841790.1343494X-RAY DIFFRACTION99.9184
2.94-3.2860.2051670.1563160X-RAY DIFFRACTION99.8499
3.286-3.7920.2191670.1592801X-RAY DIFFRACTION99.9327
3.792-4.640.1551310.1272384X-RAY DIFFRACTION99.9603
4.64-6.5440.1741230.1371877X-RAY DIFFRACTION100
6.544-61.20.158610.1681122X-RAY DIFFRACTION99.4118

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