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- PDB-6yh5: Crystal structure of chimeric carbonic anhydrase XII with 2-Chlor... -

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Basic information

Entry
Database: PDB / ID: 6yh5
TitleCrystal structure of chimeric carbonic anhydrase XII with 2-Chloro-4-[(pyrimidin-2-ylsulfanyl)acetyl]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
BENZOIC ACID / Chem-E1F / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 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)29,8305
Polymers29,2211
Non-polymers6094
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint6 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.829, 41.103, 71.699
Angle α, β, γ (deg.)90.000, 103.660, 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: 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

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Non-polymers , 5 types, 338 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.05 Å3/Da / Density % sol: 39.99 %
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: 0.826605 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826605 Å / Relative weight: 1
ReflectionResolution: 1.2→69.672 Å / Num. all: 73229 / Num. obs: 73229 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Rsym value: 0.049 / Net I/av σ(I): 8.2 / Net I/σ(I): 15.3 / Num. measured all: 494667
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
1.2-1.266.40.2922.768309105930.1350.3490.2924.798.3
1.26-1.346.90.2253.469242100640.10.2660.2256.299.1
1.34-1.436.70.1664.66319094540.0750.1970.1667.698.5
1.43-1.556.70.1146.55861387900.0520.1370.11410.398.6
1.55-1.76.90.0858.55656881510.0380.1010.0851499.3
1.7-1.96.60.062114855973670.0290.0750.06218.698.5
1.9-2.197.10.04813.54668165610.0210.0570.04826.799.7
2.19-2.686.70.04414.83661854970.020.0520.0443098.5
2.68-3.797.10.03816.33080143320.0160.0430.03837.499.4
3.79-69.6726.60.0319.81608624200.0130.0350.0338.998.8

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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: 1.2→40.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU R Cruickshank DPI: 0.0369 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.039
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.159 7367 10.1 %RANDOM
Rwork0.123 ---
obs0.1266 65836 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 104.48 Å2 / Biso mean: 17.055 Å2 / Biso min: 6.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.07 Å2
2---0.26 Å20 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.2→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 35 339 2410
Biso mean--24.38 30.73 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122232
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.6473045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7665279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27823.519108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39815363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.164158
X-RAY DIFFRACTIONr_chiral_restr0.1410.2271
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021766
X-RAY DIFFRACTIONr_rigid_bond_restr7.96332232
X-RAY DIFFRACTIONr_sphericity_free25.385186
X-RAY DIFFRACTIONr_sphericity_bonded12.38952315
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.191 569 -
Rwork0.153 4815 -
all-5384 -
obs--98.14 %

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