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- PDB-6ql3: Crystal structure of chimeric carbonic anhydrase VI with 3-(cyclo... -

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Basic information

Entry
Database: PDB / ID: 6ql3
TitleCrystal structure of chimeric carbonic anhydrase VI with 3-(cyclooctylamino)-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 / 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
BENZOIC ACID / MALONIC ACID / DI(HYDROXYETHYL)ETHER / Chem-V14 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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 1.1Jan 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)30,65511
Polymers29,3661
Non-polymers1,28910
Water4,954275
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint11 kcal/mol
Surface area11200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.209, 41.373, 71.846
Angle α, β, γ (deg.)90.000, 104.170, 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 , 8 types, 285 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Fragment: 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-V14 / 3-(cyclooctylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 444.489 Da / Num. of mol.: 1 / Fragment: Zn / Source method: obtained synthetically / Formula: C16H23F3N2O5S2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Fragment: Dimethyl sulfoxide / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Fragment: polyethylene glycol / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Fragment: ethane-1,2-diol / Source method: obtained synthetically / Formula: C3H4O4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Fragment: Malonate / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Fragment: BENZOIC ACID / Source method: obtained synthetically / Formula: C7H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.07 Å3/Da / Density % sol: 40.62 %
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: 1.35→69.659 Å / Num. all: 52382 / Num. obs: 52382 / % possible obs: 98.8 % / Redundancy: 6.8 % / Rpim(I) all: 0.039 / Rrim(I) all: 0.102 / Rsym value: 0.088 / Net I/av σ(I): 4.87 / Net I/σ(I): 10.8 / Num. measured all: 353839
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.35-1.426.70.3381.80.1510.3910.33899
1.42-1.516.70.2642.20.1180.3050.26498.5
1.51-1.616.70.2052.60.0920.2380.20598.3
1.61-1.746.70.1613.20.0730.1890.16198.3
1.74-1.916.80.124.30.0540.1410.1299.2
1.91-2.136.90.0925.70.0430.110.09299.3
2.13-2.466.90.0825.90.0360.0960.08299.4
2.46-3.026.90.0727.20.0310.0830.07299.6
3.02-4.276.80.0589.80.0250.0660.05898.5
4.27-69.6596.70.052100.0230.0590.05298.3

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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: 1.35→39.83 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.968 / SU R Cruickshank DPI: 0.0517 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.05
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1558 5161 9.9 %RANDOM
Rwork0.1163 ---
obs0.1202 52284 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 90.28 Å2 / Biso mean: 15.152 Å2 / Biso min: 3.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å2-0.29 Å2
2---0.6 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.35→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 80 275 2386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0122275
X-RAY DIFFRACTIONr_angle_refined_deg2.1951.6563098
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8175280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61223.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.622157
X-RAY DIFFRACTIONr_chiral_restr0.1270.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021793
X-RAY DIFFRACTIONr_mcbond_it1.9131.0041092
X-RAY DIFFRACTIONr_mcangle_it2.5051.5061381
X-RAY DIFFRACTIONr_scbond_it3.9151.4391183
X-RAY DIFFRACTIONr_rigid_bond_restr7.01832275
X-RAY DIFFRACTIONr_sphericity_free31.1225152
X-RAY DIFFRACTIONr_sphericity_bonded15.64752330
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 394 -
Rwork0.14 3457 -
all-3851 -
obs--98.47 %

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