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- PDB-3m67: Crystal structure of human carbonic anhydrase isozyme II with 2-c... -

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Basic information

Entry
Database: PDB / ID: 3m67
TitleCrystal structure of human carbonic anhydrase isozyme II with 2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / LYASE-LYASE INHIBITOR complex
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
Chem-E36 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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: Capkauskaite, E. / Baranauskiene, L. / Golovenko, D. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionMar 15, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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)29,9515
Polymers29,2891
Non-polymers6624
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.972, 41.007, 71.681
Angle α, β, γ (deg.)90.000, 104.430, 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) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-E36 / 2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide


Mass: 439.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H14ClN3O5S2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMETAL ION NATURALLY OCCURS IN CARBONIC ANHYDRASES
Sequence details126 IS SKIPPED IN THE NUMBERING.

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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: 39.7 %
Description: The data was collected by EMBL X13 beamline at the DORIS storage ring.
Mosaicity: 0.88 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Na-bicine pH 9.0, 2M Na-Malonate pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 17, 2009 / Details: Bent, vertically focussing mirror
RadiationMonochromator: Si [111], horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.812 Å / Relative weight: 1
ReflectionResolution: 1.8→40.656 Å / Num. all: 22174 / Num. obs: 22019 / % possible obs: 99.3 % / Redundancy: 7.5 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 31.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 7 / Num. measured all: 24150 / Num. unique all: 3191 / Rsym value: 0.222 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
MOSFLMdata reduction
SCALA3.2.19data scaling
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NNO

2nno


Resolution: 1.8→25.13 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.216 / WRfactor Rwork: 0.169 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.852 / SU B: 2.949 / SU ML: 0.094 / SU R Cruickshank DPI: 0.153 / SU Rfree: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2209 10 %RANDOM
Rwork0.176 ---
obs0.181 22008 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 50.06 Å2 / Biso mean: 18.913 Å2 / Biso min: 5.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.11 Å2
2---1 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→25.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 37 158 2244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0222207
X-RAY DIFFRACTIONr_angle_refined_deg2.0611.9653009
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9845271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.82724.706102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.316157
X-RAY DIFFRACTIONr_chiral_restr0.1580.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021716
X-RAY DIFFRACTIONr_nbd_refined0.2220.2953
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2132
X-RAY DIFFRACTIONr_metal_ion_refined0.0620.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.227
X-RAY DIFFRACTIONr_mcbond_it1.4391.51374
X-RAY DIFFRACTIONr_mcangle_it2.03222132
X-RAY DIFFRACTIONr_scbond_it3.01731020
X-RAY DIFFRACTIONr_scangle_it4.2084.5872
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 148 -
Rwork0.224 1455 -
all-1603 -
obs--99.38 %

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