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- PDB-9s4g: Carbonic anhydrases from Candida parapsilosis -

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Basic information

Entry
Database: PDB / ID: 9s4g
TitleCarbonic anhydrases from Candida parapsilosis
ComponentsCarbonic anhydrase
KeywordsLYASE / Carbonic anhydrases / Candida parapsilosis / acetazolamide
Function / homology
Function and homology information


cellular response to carbon dioxide / carbon utilization / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / zinc ion binding / cytoplasm
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Domain/homology
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsDostal, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)LX22NPO5103European Union
CitationJournal: J Struct Biol X / Year: 2025
Title: Structural characterization and inhibition of carbonic anhydrase from Candida parapsilosis.
Authors: Dostal, J. / Uhrova, Z. / Skrlova, M. / Machacek, S. / Clarova, K. / Lepsik, M. / Bulvas, O. / Vrabel, M. / Heidingsfeld, O. / Pichova, I.
History
DepositionJul 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase
B: Carbonic anhydrase
C: Carbonic anhydrase
D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,04312
Polymers102,8924
Non-polymers1,1518
Water19811
1
A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0226
Polymers51,4462
Non-polymers5754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7610 Å2
ΔGint-125 kcal/mol
Surface area16560 Å2
2
C: Carbonic anhydrase
D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0226
Polymers51,4462
Non-polymers5754
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7780 Å2
ΔGint-121 kcal/mol
Surface area16640 Å2
Unit cell
Length a, b, c (Å)118.788, 118.788, 188.214
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
Carbonic anhydrase / Carbonate dehydratase


Mass: 25723.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: NCE103, CPAR2_101880 / Production host: Escherichia coli (E. coli) / References: UniProt: G8B6R8, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn
#3: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.23 Å3/Da / Density % sol: 61.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium acetate (pH 5.0), 7.5 % (w/v) PEG 6000, 20% glycerol w
PH range: 4.8-5.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 5, 2022
RadiationMonochromator: 0.9184 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.701→41.05 Å / Num. obs: 35198 / % possible obs: 93.11 % / Redundancy: 1.99 % / Biso Wilson estimate: 70.93 Å2 / CC1/2: 1 / Net I/σ(I): 15.96
Reflection shellResolution: 2.701→2.798 Å / Num. unique obs: 3693 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→41.05 Å / SU ML: 0.4623 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3288 1757 5.01 %
Rwork0.2723 33363 -
obs0.272 35198 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.91 Å2
Refinement stepCycle: LAST / Resolution: 2.701→41.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5769 0 56 11 5836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00435941
X-RAY DIFFRACTIONf_angle_d0.81938155
X-RAY DIFFRACTIONf_chiral_restr0.0423959
X-RAY DIFFRACTIONf_plane_restr0.00341077
X-RAY DIFFRACTIONf_dihedral_angle_d9.2676858
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.701-2.7980.47211430.45452686X-RAY DIFFRACTION99.47
2.77-2.860.41541410.36942698X-RAY DIFFRACTION99.68
2.86-2.950.40231420.33392697X-RAY DIFFRACTION99.82
2.95-3.050.36241430.3112711X-RAY DIFFRACTION99.51
3.05-3.180.3481420.29742689X-RAY DIFFRACTION99.54
3.18-3.320.35811440.32712736X-RAY DIFFRACTION99.83
3.32-3.490.3575920.32661757X-RAY DIFFRACTION64.63
3.49-3.710.32091030.28861953X-RAY DIFFRACTION71.36
3.71-40.3281120.26482118X-RAY DIFFRACTION77.48
4-4.40.34351450.23692759X-RAY DIFFRACTION99.9
4.4-5.040.27041460.22432763X-RAY DIFFRACTION99.9
5.04-6.340.30441480.27512824X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 31.0000805451 Å / Origin y: -27.453294815 Å / Origin z: 2.07595092831 Å
111213212223313233
T0.652540348489 Å2-0.281536613283 Å2-0.123387178946 Å2-0.710167099635 Å20.102391399916 Å2--0.971538709856 Å2
L1.4930805913 °21.35686245059 °2-0.134783581317 °2-1.92311337399 °2-0.00575789421236 °2--0.391033080084 °2
S-0.0284909462645 Å °0.0299281489585 Å °-0.0698310215057 Å °-0.0381386341767 Å °0.0179517279847 Å °0.123209628527 Å °0.0704134234005 Å °-0.0758896849942 Å °-0.000141957877622 Å °
Refinement TLS groupSelection details: all

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