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- PDB-4ruy: Crystal structure of human Carbonic Anhydrase II in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4ruy
TitleCrystal structure of human Carbonic Anhydrase II in complex with 4-propoxybenzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / metalloenzyme / analgesic
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 / positive regulation of synaptic transmission, GABAergic ...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 / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / 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
4-propoxybenzenesulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsPinard, M.A. / Mckenna, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2015
Title: A class of sulfonamide carbonic anhydrase inhibitors with neuropathic pain modulating effects.
Authors: Carta, F. / Di Cesare Mannelli, L. / Pinard, M. / Ghelardini, C. / Scozzafava, A. / McKenna, R. / Supuran, C.T.
History
DepositionNov 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,8775
Polymers29,2891
Non-polymers5884
Water3,531196
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.271, 41.107, 71.663
Angle α, β, γ (deg.)90.000, 104.290, 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: 29289.062 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-3W6 / 4-propoxybenzenesulfonamide


Mass: 215.269 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13NO3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 1.6 M sodium citrate, 50 mM Tris-HCl, 3mM 4-propoxybenzenesulfonamide, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9177 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 6, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9177 Å / Relative weight: 1
ReflectionResolution: 1.14→20 Å / Num. obs: 85660 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.14-1.18194.8
1.18-1.23197.5
1.23-1.28197.6
1.28-1.35198.7
1.35-1.44198.9
1.44-1.55199.2
1.55-1.7199.5
1.7-1.95199.8
1.95-2.45199.9
2.45-20198.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→19.868 Å / SU ML: 0.13 / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 2002 2.34 %5%
Rwork0.2013 ---
obs0.2016 85636 98.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.17 Å2 / Biso mean: 12.1359 Å2 / Biso min: 3.69 Å2
Refinement stepCycle: LAST / Resolution: 1.14→19.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 35 196 2280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052175
X-RAY DIFFRACTIONf_angle_d1.1292965
X-RAY DIFFRACTIONf_chiral_restr0.078310
X-RAY DIFFRACTIONf_plane_restr0.005383
X-RAY DIFFRACTIONf_dihedral_angle_d12.72791
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.14-1.16820.27741400.24145564570493
1.1682-1.19980.22871290.2225881601097
1.1998-1.23510.24141490.20695871602098
1.2351-1.2750.20151380.20445905604398
1.275-1.32060.2171380.19565978611698
1.3206-1.37340.21481510.19425949610099
1.3734-1.43590.22241350.20286018615399
1.4359-1.51160.24781490.19776016616599
1.5116-1.60620.23871410.203859946135100
1.6062-1.73020.22291480.211960606208100
1.7302-1.90420.23491430.215360756218100
1.9042-2.17940.22711480.208161006248100
2.1794-2.74470.21551450.212361096254100
2.7447-19.87110.18211480.1786114626298
Refinement TLS params.Method: refined / Origin x: -9.6572 Å / Origin y: -1.7029 Å / Origin z: 15.9896 Å
111213212223313233
T0.0436 Å20 Å2-0.0004 Å2-0.0479 Å20.0007 Å2--0.0449 Å2
L0.148 °2-0.0647 °2-0.0086 °2-0.1433 °20.0067 °2--0.1108 °2
S-0.0072 Å °-0.024 Å °0.0067 Å °-0.0428 Å °0.0065 Å °0.0009 Å °-0.0064 Å °0.0256 Å °-0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allA262 - 301
3X-RAY DIFFRACTION1allA1 - 305
4X-RAY DIFFRACTION1allA304 - 400
5X-RAY DIFFRACTION1allA1 - 596

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