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- PDB-6ql2: Crystal structure of chimeric carbonic anhydrase VI with ethoxzol... -

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Basic information

Entry
Database: PDB / ID: 6ql2
TitleCrystal structure of chimeric carbonic anhydrase VI with ethoxzolamide.
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 / 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, 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
6-ethoxy-1,3-benzothiazole-2-sulfonamide / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Sci Rep / Year: 2019
Title: Engineered Carbonic Anhydrase VI-Mimic Enzyme Switched the Structure and Affinities of Inhibitors.
Authors: Kazokaite, J. / Kairys, V. / Smirnoviene, J. / Smirnov, A. / Manakova, E. / Tolvanen, M. / Parkkila, S. / Matulis, D.
History
DepositionJan 31, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 2.0Jan 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules

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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)30,1887
Polymers29,3661
Non-polymers8226
Water4,053225
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint3 kcal/mol
Surface area11560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.136, 41.309, 71.368
Angle α, β, γ (deg.)90.000, 104.220, 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: 29366.055 Da / Num. of mol.: 1 / Fragment: human carbonic anhydrase II / Mutation: A65T, N67Q, F130Y, V134Q, L203T
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 , 7 types, 231 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Fragment: 6-Ethoxy-1,3-benzothiazole-2-sulfonamide / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Fragment: Zn / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Fragment: Dimethyl sulfoxide / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Fragment: 2-(Bis(2-hydroxyethyl)amino)acetic acid / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Fragment: ethane-1,2-diol / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-EZL / 6-ethoxy-1,3-benzothiazole-2-sulfonamide / Ethoxzolamide


Mass: 258.317 Da / Num. of mol.: 1 / Fragment: 2-morpholin-4-ylethanesulfonic acid / Source method: obtained synthetically / Formula: C9H10N2O3S2 / Comment: medication, inhibitor*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystallization buffer was 0.1M sodium BICINE (pH 9), 0.2M ammonium sulfate and 2M sodium malonate (pH 7)

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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: P14 (MX2) / Wavelength: 0.975522 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975522 Å / Relative weight: 1
ReflectionResolution: 1.3→40.845 Å / Num. all: 56403 / Num. obs: 56403 / % possible obs: 96.4 % / Redundancy: 6.9 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.079 / Rsym value: 0.067 / Net I/av σ(I): 4.251 / Net I/σ(I): 13.1 / Num. measured all: 389087
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.3-1.376.90.33420.1450.3890.33494.5
1.37-1.456.90.2312.90.1020.2720.23194.9
1.45-1.556.90.154.50.0680.180.1595.6
1.55-1.686.70.1056.50.050.130.10595.8
1.68-1.8470.0828.10.0380.1010.08296.8
1.84-2.0670.07190.0320.0870.07197.8
2.06-2.3770.065100.0290.0780.06598.3
2.37-2.916.90.06210.30.0270.0730.06298.3
2.91-4.116.80.05810.10.0250.0670.05898.8
4.11-40.8456.60.0598.40.0260.0680.05997.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.3→39.7 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.974 / SU R Cruickshank DPI: 0.0463 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.047
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1573 5693 10.1 %RANDOM
Rwork0.1189 ---
obs0.1227 56387 95.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 109.31 Å2 / Biso mean: 20.4793 Å2 / Biso min: 5.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å20.13 Å2
2---0.35 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.3→39.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 43 226 2323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122221
X-RAY DIFFRACTIONr_angle_refined_deg1.9911.6573026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6385269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4423.578109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38715367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.838158
X-RAY DIFFRACTIONr_chiral_restr0.1280.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021725
X-RAY DIFFRACTIONr_mcbond_it2.1641.5931061
X-RAY DIFFRACTIONr_mcangle_it2.5392.4051335
X-RAY DIFFRACTIONr_scbond_it5.1172.0381160
X-RAY DIFFRACTIONr_rigid_bond_restr6.20632221
X-RAY DIFFRACTIONr_sphericity_free29.855138
X-RAY DIFFRACTIONr_sphericity_bonded16.4852242
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 414 -
Rwork0.13 3645 -
all-4059 -
obs--94.05 %

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