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- PDB-6yhc: Crystal structure of chimeric carbonic anhydrase XII with 3-(benz... -

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Basic information

Entry
Database: PDB / ID: 6yhc
TitleCrystal structure of chimeric carbonic anhydrase XII with 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / 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, 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-WWO / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Chemistryopen / Year: 2021
Title: Switching the Inhibitor-Enzyme Recognition Profile via Chimeric Carbonic Anhydrase XII.
Authors: Smirnoviene, J. / Smirnov, A. / Zaksauskas, A. / Zubriene, A. / Petrauskas, V. / Mickeviciute, A. / Michailoviene, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Baranauskiene, L. / ...Authors: Smirnoviene, J. / Smirnov, A. / Zaksauskas, A. / Zubriene, A. / Petrauskas, V. / Mickeviciute, A. / Michailoviene, V. / Capkauskaite, E. / Manakova, E. / Grazulis, S. / Baranauskiene, L. / Chen, W.Y. / Ladbury, J.E. / Matulis, D.
History
DepositionMar 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2135
Polymers29,2211
Non-polymers9924
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint2 kcal/mol
Surface area11220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.890, 40.963, 71.406
Angle α, β, γ (deg.)90.000, 103.780, 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: 29220.879 Da / Num. of mol.: 1 / Mutation: A65S, N67K, I91T, F130A, V134S, L203N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-WWO / 3-(benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 424.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15F3N2O5S2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 39.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.28→40.963 Å / Num. all: 59961 / Num. obs: 59961 / % possible obs: 98.7 % / Redundancy: 3.3 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Rsym value: 0.046 / Net I/av σ(I): 7.2 / Net I/σ(I): 9.2 / Num. measured all: 199179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.28-1.353.30.2662.72829586280.2070.3810.266398.2
1.35-1.433.30.1883.82702882170.1450.2680.1883.898.4
1.43-1.533.30.1285.32535477400.0990.1810.1285.198.6
1.53-1.653.20.09372338172140.070.1280.0936.798.7
1.65-1.813.30.0758.22220566410.0540.10.0758.998.7
1.81-2.023.40.069.92071660620.0420.0780.0612.499.1
2.02-2.343.40.05111.91835453680.0360.0660.05115.499.2
2.34-2.863.40.04413.51537745320.0310.0590.04417.299.3
2.86-4.053.40.03715.51194435480.0260.0490.0372099.1
4.05-40.9633.20.03216.2652520110.0230.0420.03220.399.6

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q09

4q09


Resolution: 1.28→40.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.97 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.048
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1721 6002 10 %RANDOM
Rwork0.1304 ---
obs0.1346 53768 98.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 103.04 Å2 / Biso mean: 21.824 Å2 / Biso min: 9.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20.57 Å2
2---1.21 Å20 Å2
3---1.43 Å2
Refinement stepCycle: final / Resolution: 1.28→40.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 59 229 2303
Biso mean--36.03 34.83 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122210
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.6723024
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9855273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58723.654104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88415345
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.449157
X-RAY DIFFRACTIONr_chiral_restr0.1280.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021739
X-RAY DIFFRACTIONr_rigid_bond_restr5.44432210
X-RAY DIFFRACTIONr_sphericity_free26.2155125
X-RAY DIFFRACTIONr_sphericity_bonded16.28852244
LS refinement shellResolution: 1.28→1.313 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 429 -
Rwork0.195 3926 -
all-4355 -
obs--97.67 %

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