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

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Basic information

Entry
Database: PDB / ID: 5jqt
TitleCrystal structure of human carbonic anhydrase II in complex with Benzoxaborole at pH 7.4
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 anion transport / secretion / cyanamide hydratase / arylesterase activity / regulation of chloride transport / angiotensin-activated signaling pathway / Reversible hydration of carbon dioxide / regulation of intracellular pH ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of anion transport / secretion / cyanamide hydratase / arylesterase activity / regulation of chloride transport / angiotensin-activated signaling pathway / Reversible hydration of carbon dioxide / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / hydro-lyase activity / 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 / apical part of cell / one-carbon metabolic process / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Alpha carbonic anhydrase / Carbonic Anhydrase II / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class, conserved site / Carbonic anhydrase, alpha-class / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Eukaryotic-type carbonic anhydrase / Alpha carbonic anhydrase domain superfamily / Alpha carbonic anhydrase domain ...Alpha carbonic anhydrase / Carbonic Anhydrase II / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class, conserved site / Carbonic anhydrase, alpha-class / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Eukaryotic-type carbonic anhydrase / Alpha carbonic anhydrase domain superfamily / Alpha carbonic anhydrase domain / Roll / Alpha Beta
Similarity search - Domain/homology
1,1-dihydroxy-1,3-dihydro-2,1-benzoxaborol-1-ium / 2,1-benzoxaborol-1(3H)-ol / 4-(HYDROXYMERCURY)BENZOIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.36 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 5, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 2.0Oct 30, 2019Group: Data collection / Derived calculations / Non-polymer description
Category: chem_comp / pdbx_struct_conn_angle / struct_conn / Item: _chem_comp.formula
Revision 2.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn

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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)30,90410
Polymers29,4771
Non-polymers1,4279
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area11950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.234, 41.104, 71.831
Angle α, β, γ (deg.)90.000, 103.920, 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: 29477.307 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 , 5 types, 244 molecules

#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.: 5 / Source method: obtained synthetically / Formula: C7H8BO3
#4: Chemical ChemComp-6M9 / 2,1-benzoxaborol-1(3H)-ol


Mass: 133.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H7BO2
#5: Chemical ChemComp-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H6HgO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 2.4 M SODIUM MALONATE

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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: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.36→69.72 Å / Num. obs: 50126 / % possible obs: 97.4 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Χ2: 1.02 / Net I/av σ(I): 20.302 / Net I/σ(I): 24.6 / Num. measured all: 183415
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.36-1.382.30.29220130.96479.1
1.38-1.412.70.27924080.99793.5
1.41-1.442.80.26223951.00894.8
1.44-1.472.90.21824310.98994.5
1.47-1.52.90.19124421.04996.8
1.5-1.5330.17124631.02996.5
1.53-1.573.10.14925241.06898.1
1.57-1.613.20.12524911.04798.1
1.61-1.663.20.11625381.04198.8
1.66-1.713.30.125641.05699.8
1.71-1.773.40.08525801.02399.8
1.77-1.853.60.07225711.02699.9
1.85-1.933.70.06425371.018100
1.93-2.033.90.05725721.047100
2.03-2.1640.05425890.988100
2.16-2.334.20.04825631.07999.8
2.33-2.564.40.04726060.99199.7
2.56-2.934.70.04925701.0499.8
2.93-3.6950.04425950.95399.5
3.69-506.30.0426741.00899.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
CrystalCleardata reduction
REFMAC5.8.0073phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2
Resolution: 1.36→69.72 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.915 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 2442 5 %RANDOM
Rwork0.121 ---
obs0.1232 46386 94.82 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 197.75 Å2 / Biso mean: 14.163 Å2 / Biso min: 4.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.7 Å2
2---0.25 Å20 Å2
3---0.47 Å2
Refinement stepCycle: final / Resolution: 1.36→69.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2073 0 83 235 2391
Biso mean--18.84 23.82 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022280
X-RAY DIFFRACTIONr_bond_other_d0.0220.022079
X-RAY DIFFRACTIONr_angle_refined_deg2.2771.9583110
X-RAY DIFFRACTIONr_angle_other_deg1.0652.9794807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9445270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46824.64699
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32115364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.035157
X-RAY DIFFRACTIONr_chiral_restr0.3520.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022636
X-RAY DIFFRACTIONr_gen_planes_other0.0320.019561
X-RAY DIFFRACTIONr_mcbond_it2.2681.1081068
X-RAY DIFFRACTIONr_mcbond_other2.2541.1031067
X-RAY DIFFRACTIONr_mcangle_it2.7721.6691342
X-RAY DIFFRACTIONr_rigid_bond_restr3.74534358
X-RAY DIFFRACTIONr_sphericity_free27.566563
X-RAY DIFFRACTIONr_sphericity_bonded13.27854445
LS refinement shellResolution: 1.361→1.397 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 140 -
Rwork0.169 2690 -
all-2830 -
obs--74.95 %

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