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- PDB-4ww6: Crystal structure of human carbonic anhydrase isozyme II with 2,3... -

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Basic information

Entry
Database: PDB / ID: 4ww6
TitleCrystal structure of human carbonic anhydrase isozyme II with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-3TV / MALONIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.06 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Biophys.Chem. / Year: 2015
Title: Intrinsic thermodynamics of 4-substituted-2,3,5,6-tetrafluorobenzenesulfonamide binding to carbonic anhydrases by isothermal titration calorimetry.
Authors: Zubriene, A. / Smirnoviene, J. / Smirnov, A. / Morkunaite, V. / Michailoviene, V. / Jachno, J. / Juozapaitiene, V. / Norvaisas, P. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionNov 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5028
Polymers29,2891
Non-polymers1,2137
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint6 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.214, 41.026, 71.774
Angle α, β, γ (deg.)90.000, 104.290, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 7 types, 275 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Fragment: 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Fragment: ZINC ION / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Fragment: BICINE / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Fragment: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / Source method: obtained synthetically / Formula: C3H4O4
#6: Chemical ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 1 / Fragment: DIMETHYL SULFOXIDE / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Chemical ChemComp-3TV / 2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide


Mass: 303.297 Da / Num. of mol.: 2 / Fragment: MALONIC ACID / Source method: obtained synthetically / Formula: C9H9F4NO2S2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.25 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 1.06→69.554 Å / Num. all: 102717 / Num. obs: 102717 / % possible obs: 95.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 8.784 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.05 / Rsym value: 0.041 / Net I/av σ(I): 6.933 / Net I/σ(I): 17.9 / Num. measured all: 676004
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueDiffraction-IDNet I/σ(I) obs% possible all
1.06-1.125.80.4280.352.275329129520.170.430.3514.183
1.12-1.196.40.2830.2333.389091139680.110.280.2336.394.6
1.19-1.276.70.20.1664.690220134490.080.20.1668.596.6
1.27-1.376.50.1440.1166.581656126240.050.140.11611.297.1
1.37-1.56.90.1030.0819.281100117330.040.10.08115.598.4
1.5-1.686.60.0740.05612.969678106150.030.070.0562198.2
1.68-1.947.10.0540.04116.36745795310.020.050.0413099.5
1.94-2.376.60.0450.03518.75294180130.020.050.03537.598.8
2.37-3.357.10.040.03218.84479762960.010.040.03244.999.7
3.35-69.556.70.0370.03116.82373535360.010.040.03148.299.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.006data extraction
SCALAdata scaling
Cootmodel building
MOLREPphasing
REFMAC5.6.0117refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.06→40.91 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.13 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.937 / SU R Cruickshank DPI: 0.028 / SU Rfree: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.151 10363 10.1 %RANDOM
Rwork0.128 92334 --
obs0.131 102697 95.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 105.69 Å2 / Biso mean: 15.737 Å2 / Biso min: 6.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.1 Å2
2---0.27 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.06→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 67 268 2384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.022396
X-RAY DIFFRACTIONr_angle_refined_deg2.4171.9783282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1675303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61824.815108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97615383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.597159
X-RAY DIFFRACTIONr_chiral_restr0.1620.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211913
X-RAY DIFFRACTIONr_rigid_bond_restr8.83532396
X-RAY DIFFRACTIONr_sphericity_free20.8845269
X-RAY DIFFRACTIONr_sphericity_bonded9.79552316
LS refinement shellResolution: 1.06→1.088 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 595 -
Rwork0.192 5222 -
all-5817 -
obs--73.24 %

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