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- PDB-3m96: Crystal structure of human carbonic anhydrase isozyme II with 5-{... -

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Basic information

Entry
Database: PDB / ID: 3m96
TitleCrystal structure of human carbonic anhydrase isozyme II with 5-{[(5-bromo-1H-benzimidazol-2-yl)sulfanyl]acetyl}-2-chlorobenzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide
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
Chem-E38 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsGrazulis, S. / Manakova, E. / Golovenko, D.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Indapamide-like benzenesulfonamides as inhibitors of carbonic anhydrases I, II, VII, and XIII.
Authors: Baranauskiene, L. / Golovenko, D. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionMar 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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)29,9715
Polymers29,2891
Non-polymers6824
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.050, 40.921, 71.468
Angle α, β, γ (deg.)90.000, 104.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


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 (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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-E38 / 5-{[(5-bromo-1H-benzimidazol-2-yl)sulfanyl]acetyl}-2-chlorobenzenesulfonamide


Mass: 460.753 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H11BrClN3O3S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9.0, 0.2 M ammonium sulfate and 2M sodium malonate, pH 7.0 made from 1M sodium BICINE and 3.4M sodium malonate, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.9443 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2009
RadiationMonochromator: Double crystal Si(111), horizontally focussing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9443 Å / Relative weight: 1
ReflectionResolution: 1.4→28.884 Å / Num. all: 46670 / Num. obs: 46297 / % possible obs: 99.2 % / Redundancy: 9.3 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 22.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 4.4 / Num. measured all: 49268 / Num. unique all: 6614 / Rsym value: 0.253 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.25data scaling
PDB_EXTRACT3.006data extraction
MAR345data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HLJ

3hlj


Resolution: 1.4→28.47 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.877 / SU B: 1.049 / SU ML: 0.043 / SU R Cruickshank DPI: 0.069 / SU Rfree: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 4647 10 %RANDOM
Rwork0.176 ---
obs0.18 46284 99.23 %-
all-46670 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.97 Å2 / Biso mean: 15.552 Å2 / Biso min: 5.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20.11 Å2
2---0.51 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.4→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 34 239 2322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0222188
X-RAY DIFFRACTIONr_angle_refined_deg2.5871.9652980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39324.69498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32515359
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.122157
X-RAY DIFFRACTIONr_chiral_restr0.1860.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021695
X-RAY DIFFRACTIONr_nbd_refined0.2260.21062
X-RAY DIFFRACTIONr_nbtor_refined0.3250.21482
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2205
X-RAY DIFFRACTIONr_metal_ion_refined0.0780.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.258
X-RAY DIFFRACTIONr_mcbond_it1.841.51360
X-RAY DIFFRACTIONr_mcangle_it2.47422135
X-RAY DIFFRACTIONr_scbond_it3.3093990
X-RAY DIFFRACTIONr_scangle_it4.8794.5845
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 334 -
Rwork0.278 2989 -
all-3323 -
obs--98.26 %

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