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- PDB-8q18: The Crystal Structure of Human Carbonic Anhydrase IX in Complex w... -

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Basic information

Entry
Database: PDB / ID: 8q18
TitleThe Crystal Structure of Human Carbonic Anhydrase IX in Complex with Sulfonamide
ComponentsCarbonic anhydrase 9
KeywordsLYASE / CA IX / CA 9 / carbonic anhydrase IX / carbonic anhydrase 9
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / zinc ion binding / membrane / 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
Chem-IQE / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsLeitans, J. / Tars, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chemmedchem / Year: 2023
Title: Structural Basis of Saccharin Derivative Inhibition of Carbonic Anhydrase IX.
Authors: Leitans, J. / Kazaks, A. / Bogans, J. / Supuran, C.T. / Akopjana, I. / Ivanova, J. / Zalubovskis, R. / Tars, K.
History
DepositionJul 31, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 20, 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 9
B: Carbonic anhydrase 9
C: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,84316
Polymers112,7474
Non-polymers2,09612
Water12,592699
1
A: Carbonic anhydrase 9
hetero molecules

C: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4218
Polymers56,3732
Non-polymers1,0486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-y-1/3,x-y+1/3,z+1/31
Buried area2200 Å2
ΔGint-21 kcal/mol
Surface area20570 Å2
2
B: Carbonic anhydrase 9
D: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4218
Polymers56,3732
Non-polymers1,0486
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-19 kcal/mol
Surface area20520 Å2
Unit cell
Length a, b, c (Å)152.100, 152.100, 171.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-436-

HOH

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Components

#1: Protein
Carbonic anhydrase 9 / Carbonate dehydratase IX / Carbonic anhydrase IX / CA-IX / CAIX / Membrane antigen MN / P54/58N / ...Carbonate dehydratase IX / Carbonic anhydrase IX / CA-IX / CAIX / Membrane antigen MN / P54/58N / Renal cell carcinoma-associated antigen G250 / RCC-associated antigen G250 / pMW1


Mass: 28186.711 Da / Num. of mol.: 4 / Mutation: C41S, N213Q
Source method: isolated from a genetically manipulated source
Details: two dimers / Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Cell line (production host): Pichia pastoris / Production host: Komagataella pastoris (fungus) / References: UniProt: Q16790, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IQE / 1,1,3-tris(oxidanylidene)-2-(2-phenylethyl)-1,2-benzothiazole-6-sulfonamide


Mass: 366.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H14N2O5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 699 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.41 Å3/Da / Density % sol: 63.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 9 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% ...Details: CRYSTALLIZATION CONDITIONS: 1.0 M DI-AMMONIUM HYDROGEN PHOSPHATE, 0.1 M SODIUM ACETATE PH 4.5, PROTEIN 9 MG/ML, 5-10 MM INHIBITOR (STOCK SOLUTION WAS 100 MM INHIBITOR DISSOLVED IN 100% DIMETHYL SULFOXIDE), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.97898 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 2015 / Details: MULTILAYER
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97898 Å / Relative weight: 1
ReflectionResolution: 2.13→61.49 Å / Num. obs: 81224 / % possible obs: 98.1 % / Redundancy: 2 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.6
Reflection shellResolution: 2.13→2.25 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 2 / Num. unique obs: 12025 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→61.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.182 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21742 4080 5 %RANDOM
Rwork0.17517 ---
obs0.17734 77139 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.732 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å20 Å2
2--0.42 Å2-0 Å2
3----1.38 Å2
Refinement stepCycle: 1 / Resolution: 2.13→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7696 0 124 699 8519
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0128092
X-RAY DIFFRACTIONr_bond_other_d0.0090.0167131
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.66211085
X-RAY DIFFRACTIONr_angle_other_deg0.5191.54616634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.14251004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.9981063
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.105101144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0670.21186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029340
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021608
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2463.74019
X-RAY DIFFRACTIONr_mcbond_other3.2463.74019
X-RAY DIFFRACTIONr_mcangle_it5.115.5315019
X-RAY DIFFRACTIONr_mcangle_other5.115.5315020
X-RAY DIFFRACTIONr_scbond_it3.6864.0144073
X-RAY DIFFRACTIONr_scbond_other3.6864.0144074
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6895.9446066
X-RAY DIFFRACTIONr_long_range_B_refined8.67749.4528751
X-RAY DIFFRACTIONr_long_range_B_other8.63747.5528583
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 322 -
Rwork0.279 5805 -
obs--99.43 %

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