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- PDB-6r6j: Crystal structure of human carbonic anhydrase isozyme II with 2-(... -

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Basic information

Entry
Database: PDB / ID: 6r6j
TitleCrystal structure of human carbonic anhydrase isozyme II with 2-(benzenesulfonyl)-4-chloro-N-(2-hydroxyethyl)-5-sulfamoyl-benzamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / 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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / 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, 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-JTW / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Halogenated and di-substituted benzenesulfonamides as selective inhibitors of carbonic anhydrase isoforms.
Authors: Zaksauskas, A. / Capkauskaite, E. / Jezepcikas, L. / Linkuviene, V. / Paketuryte, V. / Smirnov, A. / Leitans, J. / Kazaks, A. / Dvinskis, E. / Manakova, E. / Grazulis, S. / Tars, K. / Matulis, D.
History
DepositionMar 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: database_2 / pdbx_contact_author / pdbx_database_proc
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0475
Polymers29,2891
Non-polymers7584
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint8 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.949, 41.070, 71.542
Angle α, β, γ (deg.)90.000, 104.140, 90.000
Int Tables number4
Space group name H-MP1211

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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 / Fragment: human carbonic anhydrase II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 186 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-JTW / 4-chloranyl-~{N}-(2-hydroxyethyl)-2-(phenylsulfonyl)-5-sulfamoyl-benzamide


Mass: 418.872 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15ClN2O6S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer: 0.1M sodium bicine (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.91 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.55→40.679 Å / Num. all: 34169 / Num. obs: 34169 / % possible obs: 99 % / Redundancy: 3.2 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.07 / Rsym value: 0.049 / Net I/av σ(I): 10.269 / Net I/σ(I): 9.6 / Num. measured all: 107711
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.55-1.6330.3472.248540.290.5230.34797
1.63-1.733.10.245346690.2010.3610.24598.5
1.73-1.853.10.1584.543750.1320.2350.15898.8
1.85-23.20.1026.441260.0850.1480.10299.1
2-2.193.20.0758.238060.0620.1090.07599.7
2.19-2.453.20.0629.334790.0510.0890.06299.6
2.45-2.833.20.04911.930590.0410.070.04999.8
2.83-3.473.20.03315.826140.0280.0490.033100
3.47-4.93.20.02422.920290.0190.0340.024100
4.9-40.67930.02226.311580.0170.0310.02299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 1.55→34.69 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.1015 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2233 3410 10.1 %RANDOM
Rwork0.188 ---
obs0.1915 33894 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 62.94 Å2 / Biso mean: 18.9587 Å2 / Biso min: 7.33 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20.06 Å2
2---1.65 Å20 Å2
3---1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 39 182 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122238
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.673049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4595269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83723.578109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82515366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.236158
X-RAY DIFFRACTIONr_chiral_restr0.140.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021748
X-RAY DIFFRACTIONr_mcbond_it1.8361.6871061
X-RAY DIFFRACTIONr_mcangle_it2.7042.5221335
X-RAY DIFFRACTIONr_scbond_it2.5131.8881177
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 247 -
Rwork0.251 2218 -
all-2465 -
obs--96.55 %

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