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- PDB-4knj: Crystal structure of human carbonic anhydrase isozyme II with 2-C... -

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Basic information

Entry
Database: PDB / ID: 4knj
TitleCrystal structure of human carbonic anhydrase isozyme II with 2-Chloro-4-[(pyrimidin-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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
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-E1F / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Bioorg.Med.Chem. / Year: 2013
Title: Benzenesulfonamides with pyrimidine moiety as inhibitors of human carbonic anhydrases I, II, VI, VII, XII, and XIII
Authors: Capkauskaite, E. / Zubriene, A. / Smirnov, A. / Torresan, J. / Kisonaite, M. / Kazokaite, J. / Gylyte, J. / Michailoviene, V. / Jogaite, V. / Manakova, E. / Grazulis, S. / Tumkevicius, S. / Matulis, D.
History
DepositionMay 10, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Refinement description / Category: diffrn_detector / software / Item: _diffrn_detector.detector / _software.version
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _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)29,9725
Polymers29,2891
Non-polymers6834
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.988, 40.914, 71.339
Angle α, β, γ (deg.)90.000, 104.140, 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: 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

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Non-polymers , 5 types, 160 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-E1F / 2-chloro-4-[(pyrimidin-2-ylsulfanyl)acetyl]benzenesulfonamide


Mass: 343.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H10ClN3O3S2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / 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: 2.1 Å3/Da / Density % sol: 39.7 % / Mosaicity: 0.9 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.2M sodium malonate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: MAR555 FLAT PANEL / Detector: IMAGE PLATE / Date: Nov 21, 2011 / Details: Detector swing-out angle up to 30 degrees
RadiationMonochromator: Si (111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 2→30.26 Å / Num. obs: 15098 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 21.207 Å2 / Rsym value: 0.11 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.113.80.3880.3171.4800921350.190.390.3173.792.5
2.11-2.243.70.2960.2432.1768920650.140.30.2434.694.3
2.24-2.393.80.2360.1952.7736219570.110.240.1955.494.9
2.39-2.583.80.2040.173.3691618160.10.20.175.994.3
2.58-2.834.10.1640.1354.5693017090.080.160.1357.195.2
2.83-3.164.20.1370.115.5647015330.060.140.118.395.3
3.16-3.654.20.1170.0946.1571613580.050.120.0949.395.3
3.65-4.474.20.10.0816.7483011540.050.10.0819.995
4.47-6.324.10.0840.0688.636708860.040.080.0689.794.8
6.32-30.263.80.1080.084518354850.050.110.0849.289.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.006data extraction
DNAdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HLJ

3hlj


Resolution: 2→30.26 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.844 / SU R Cruickshank DPI: 0.247 / SU Rfree: 0.197 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1465 9.7 %RANDOM
Rwork0.164 ---
all0.171 15077 --
obs0.171 15077 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.83 Å2 / Biso mean: 18.888 Å2 / Biso min: 5.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å2-0.07 Å2
2---1.24 Å20 Å2
3---1.38 Å2
Refinement stepCycle: LAST / Resolution: 2→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 33 156 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222181
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9622960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7675262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10424.7100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.919157
X-RAY DIFFRACTIONr_chiral_restr0.1380.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021681
X-RAY DIFFRACTIONr_nbd_refined0.2250.21072
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2175
X-RAY DIFFRACTIONr_metal_ion_refined0.0670.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.223
X-RAY DIFFRACTIONr_mcbond_it1.1191.51303
X-RAY DIFFRACTIONr_mcangle_it1.83322105
X-RAY DIFFRACTIONr_scbond_it2.8723878
X-RAY DIFFRACTIONr_scangle_it4.2434.5855
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 105 -
Rwork0.204 949 -
all-1054 -
obs--92.21 %

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