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- PDB-8rj2: Crystal structure of carbonic anhydrase II with N-butyl-4-chloro-... -

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Basic information

Entry
Database: PDB / ID: 8rj2
TitleCrystal structure of carbonic anhydrase II with N-butyl-4-chloro-2-(cyclohexylsulfanyl)-5-sulfamoylbenzamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / DRUG DESIGN / CARBONIC ANHYDRASE / BENZENESULFONAMIDE / 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 / 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
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsSmirnov, A. / Manakova, E.N. / Grazulis, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Iucrj / Year: 2024
Title: From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system.
Authors: Paketuryte-Latve, V. / Smirnov, A. / Manakova, E. / Baranauskiene, L. / Petrauskas, V. / Zubriene, A. / Matuliene, J. / Dudutiene, V. / Capkauskaite, E. / Zaksauskas, A. / Leitans, J. / ...Authors: Paketuryte-Latve, V. / Smirnov, A. / Manakova, E. / Baranauskiene, L. / Petrauskas, V. / Zubriene, A. / Matuliene, J. / Dudutiene, V. / Capkauskaite, E. / Zaksauskas, A. / Leitans, J. / Grazulis, S. / Tars, K. / Matulis, D.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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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)30,0015
Polymers29,2891
Non-polymers7124
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint4 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.067, 41.148, 72.028
Angle α, β, γ (deg.)90.00, 104.15, 90.00
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
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, 270 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-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-YNF / ~{N}-butyl-4-chloranyl-2-cyclohexylsulfanyl-5-sulfamoyl-benzamide


Mass: 404.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25ClN2O3S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.01 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1M sodium bicine (pH 9) and 2M sodium malonate (pH 7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.975522 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975522 Å / Relative weight: 1
ReflectionResolution: 1.12→40.79 Å / Num. obs: 81344 / % possible obs: 89.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Net I/σ(I): 25.1 / Num. measured all: 557298
Reflection shellResolution: 1.12→1.18 Å / % possible obs: 60.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.145 / Num. measured all: 49623 / Num. unique obs: 7994 / Rpim(I) all: 0.069 / Rrim(I) all: 0.175 / Net I/σ(I) obs: 10.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
SCALAdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→40.79 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.961 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17601 8188 10.1 %RANDOM
Rwork0.14893 ---
obs0.15163 73141 88.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.582 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20.08 Å2
2---0.41 Å20 Å2
3----0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.12→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2041 0 41 266 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122266
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.6523094
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8965282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89123.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42615371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.025157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021781
X-RAY DIFFRACTIONr_gen_planes_other
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_it8.5761.4161095
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.4252.1251388
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.4981.7111171
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.12320.8813583
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr30.33832266
X-RAY DIFFRACTIONr_sphericity_free21.0945143
X-RAY DIFFRACTIONr_sphericity_bonded17.76452316
LS refinement shellResolution: 1.122→1.151 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 330 -
Rwork0.179 2969 -
obs--48.88 %

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