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- PDB-5jq0: Crystal structure of human carbonic anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5jq0
TitleCrystal structure of human carbonic anhydrase II in complex with Benzoxaborole at pH=8.7
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Benzoxaborole / Boron / Zinc / Carbonate Dehydratase
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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / 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 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
1,1-dihydroxy-1,3-dihydro-2,1-benzoxaborol-1-ium / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.4 Å
AuthorsAlterio, V. / Esposito, D. / Di Fiore, A. / De Simone, G.
CitationJournal: Chem.Commun.(Camb.) / Year: 2016
Title: Benzoxaborole as a new chemotype for carbonic anhydrase inhibition.
Authors: Alterio, V. / Cadoni, R. / Esposito, D. / Vullo, D. / Fiore, A.D. / Monti, S.M. / Caporale, A. / Ruvo, M. / Sechi, M. / Dumy, P. / Supuran, C.T. / Simone, G. / Winum, J.Y.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 30, 2019Group: Data collection / Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Jan 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)29,6943
Polymers29,4771
Non-polymers2162
Water4,288238
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.350, 41.190, 72.030
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29477.307 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pETM13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6M4 / 1,1-dihydroxy-1,3-dihydro-2,1-benzoxaborol-1-ium


Mass: 150.948 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8BO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.7 / Details: SODIUM CITRATE 1.3M, TRIS-HCL 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 42313 / % possible obs: 89.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 31.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.7 / % possible all: 74.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
REFMACphasing
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.4→50 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.576 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1461 2082 5 %RANDOM
Rwork0.1054 ---
obs0.1075 39512 87.51 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 81.11 Å2 / Biso mean: 13.898 Å2 / Biso min: 4.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0 Å20.31 Å2
2---0.3 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 23 238 2310
Biso mean--11.55 25.14 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192258
X-RAY DIFFRACTIONr_bond_other_d0.0010.022072
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.9463082
X-RAY DIFFRACTIONr_angle_other_deg0.8362.9924814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5235281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48624.762105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99515373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.047158
X-RAY DIFFRACTIONr_chiral_restr0.1040.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212650
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02537
X-RAY DIFFRACTIONr_mcbond_it1.8071.0761091
X-RAY DIFFRACTIONr_mcbond_other1.7971.0721090
X-RAY DIFFRACTIONr_mcangle_it2.2021.6241383
X-RAY DIFFRACTIONr_rigid_bond_restr2.67334330
X-RAY DIFFRACTIONr_sphericity_free25.373562
X-RAY DIFFRACTIONr_sphericity_bonded9.96854424
LS refinement shellResolution: 1.401→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.156 137 -
Rwork0.105 2270 -
all-2407 -
obs--69.35 %

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