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- PDB-7nzs: Crystal structure of chimeric carbonic anhydrase VA with 2,3,5,6-... -

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Basic information

Entry
Database: PDB / ID: 7nzs
TitleCrystal structure of chimeric carbonic anhydrase VA with 2,3,5,6-tetrafluoro-4-(propylsulfanyl)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 / 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 / cyanamide hydratase activity / 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 / 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
Chem-3TV / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: To Be Published
Title: Crystal structure of chimeric carbonic anhydrase VA
Authors: Smirnov, A.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)30,4547
Polymers29,3771
Non-polymers1,0766
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint4 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.130, 41.304, 71.250
Angle α, β, γ (deg.)90.000, 104.180, 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: 29377.160 Da / Num. of mol.: 1 / Mutation: N62T, H64Y, A65L, N67Q, I91K, F130Y, L203T
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, 267 molecules

#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-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Chemical ChemComp-3TV / 2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide


Mass: 303.297 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9F4NO2S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 39.88 %
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 / 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: 1.5→69.078 Å / Num. all: 38049 / Num. obs: 38049 / % possible obs: 99.4 % / Redundancy: 6.7 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Rsym value: 0.047 / Net I/av σ(I): 9.1 / Net I/σ(I): 17.5 / Num. measured all: 254707
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
1.5-1.586.70.2343.13699755160.1050.2760.234699.4
1.58-1.686.30.1694.33274151910.0790.2010.1697.499
1.68-1.796.80.1235.73365249430.0550.1450.1231099.6
1.79-1.946.80.0897.43119845650.040.1050.08913.799.6
1.94-2.126.40.0689.62708442160.0310.080.0681899.1
2.12-2.377.10.05511.72706938380.0240.0650.05522.999.6
2.37-2.746.90.048132341733840.0220.0570.04826.699.6
2.74-3.356.50.04114.41868428780.0190.0490.04131.999.5
3.35-4.746.90.03317.61560622490.0150.0390.03340.599.6
4.74-69.0786.50.02719.2825912690.0130.0340.02737.499.1

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.5→40.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 3806 10 %RANDOM
Rwork0.1692 ---
obs0.1725 34218 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.36 Å2 / Biso mean: 19.408 Å2 / Biso min: 6.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20.33 Å2
2---0.63 Å20 Å2
3---0.42 Å2
Refinement stepCycle: final / Resolution: 1.5→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 63 261 2358
Biso mean--35.21 30.43 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122237
X-RAY DIFFRACTIONr_angle_refined_deg1.971.6653056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3375274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73523.364107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46315350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.807158
X-RAY DIFFRACTIONr_chiral_restr0.1290.2269
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021759
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 282 -
Rwork0.214 2507 -
all-2789 -
obs--99.22 %

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