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- PDB-6rvl: Crystal structure of hCA II with Urea, N-(1,3-dihydro-1-hydroxy-2... -

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Basic information

Entry
Database: PDB / ID: 6rvl
TitleCrystal structure of hCA II with Urea, N-(1,3-dihydro-1-hydroxy-2,1-benzoxaborol-6-yl)-?N'-phenyl-
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Protein-inhibitor binding
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, 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-KKE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.72 Å
AuthorsDi Fiore, A. / De Simone, G.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2019
Title: Exploring benzoxaborole derivatives as carbonic anhydrase inhibitors: a structural and computational analysis reveals their conformational variability as a tool to increase enzyme selectivity.
Authors: Langella, E. / Alterio, V. / D'Ambrosio, K. / Cadoni, R. / Winum, J.Y. / Supuran, C.T. / Monti, S.M. / De Simone, G. / Di Fiore, A.
History
DepositionMay 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8443
Polymers29,4771
Non-polymers3672
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.450, 41.460, 72.010
Angle α, β, γ (deg.)90.000, 104.500, 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 / Production host: Escherichia coli (E. coli) / 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-KKE / 1-[1,1-bis(oxidanyl)-3~{H}-2,1-benzoxaborol-1-ium-6-yl]-3-phenyl-thiourea


Mass: 301.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14BN2O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.3 M sodium citrate, 0.1 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.72→25.4 Å / Num. obs: 24550 / % possible obs: 94.3 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.05 / Rrim(I) all: 0.105 / Χ2: 1.042 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.752.40.42310240.7160.3280.5381.00780.1
1.75-1.782.40.41110440.7220.3170.5221.07882.1
1.78-1.822.40.36310920.7920.2760.4581.07484.1
1.82-1.852.50.29611310.8750.2230.3721.08485.2
1.85-1.892.50.25411060.870.1880.3181.09587.5
1.89-1.942.60.22511310.8950.1650.2811.07688.3
1.94-1.992.60.19111910.9250.1390.2381.06891.3
1.99-2.042.70.17211760.9360.1250.2141.09192
2.04-2.12.80.16612630.9460.1170.2041.08696.9
2.1-2.1730.15312710.9580.1020.1851.05898.7
2.17-2.243.40.14813060.9610.0920.1761.06199.5
2.24-2.333.60.13512830.9670.0810.1581.046100
2.33-2.443.80.1313100.9710.0750.151.041100
2.44-2.574.10.12413140.9750.070.1431.069100
2.57-2.734.50.11912800.9770.0640.1361.037100
2.73-2.945.20.11313040.9810.0550.1261.098100
2.94-3.245.80.09713210.9860.0440.1071.085100
3.24-3.715.80.07313150.9850.0340.080.97599.9
3.71-4.675.80.0613280.9890.0280.0660.94199.9
4.67-25.45.60.04913600.9940.0230.0541.00999.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.25data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1CA2

1ca2


Resolution: 1.72→25.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2093 1007 3.9 %
Rwork0.1758 --
obs-23408 90 %
Solvent computationBsol: 47.3611 Å2
Displacement parametersBiso max: 37.8 Å2 / Biso mean: 12.7683 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-0.104 Å20 Å2-0.177 Å2
2---0.128 Å20 Å2
3---0.024 Å2
Refinement stepCycle: final / Resolution: 1.72→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 22 156 2217
Biso mean--11.24 21.47 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.57
X-RAY DIFFRACTIONc_mcbond_it1.2531.5
X-RAY DIFFRACTIONc_scbond_it2.1232
X-RAY DIFFRACTIONc_mcangle_it1.8072
X-RAY DIFFRACTIONc_scangle_it3.0842.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.72-1.780.2628880.25611702179070.1
1.78-1.850.2259800.20931890197075.2
1.85-1.940.2341920.19211979207181
1.94-2.040.21741180.16952128224687.3
2.04-2.170.1885890.17022348243794.1
2.17-2.330.21761020.17412413251596.9
2.33-2.570.21651130.17492426253997.2
2.57-2.940.21251050.1782450255598.7
2.94-3.70.20931040.17272508261299.2
3.7-25.40.18211160.15732557267399.3
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_mod.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ion_patch.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6rc73_csd.param

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