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- PDB-7nzw: Crystal structure of chimeric carbonic anhydrase VA with 4-[(4,6-... -

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Basic information

Entry
Database: PDB / ID: 7nzw
TitleCrystal structure of chimeric carbonic anhydrase VA with 4-[(4,6-dimethylpyrimidin-2-yl)thio]-2,3,5,6-tetrafluorobenzenesulfonamide
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-V50 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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)29,9115
Polymers29,3771
Non-polymers5344
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-4 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.222, 41.289, 71.468
Angle α, β, γ (deg.)90.000, 104.200, 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, 265 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-V50 / 4-[(4,6-dimethylpyrimidin-2-yl)thio]-2,3,5,6-tetrafluorobenzenesulfonamide


Mass: 367.342 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9F4N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 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: 2.06 Å3/Da / Density % sol: 40.17 %
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: 1.45→69.285 Å / Num. all: 42212 / Num. obs: 42212 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rpim(I) all: 0.023 / Rrim(I) all: 0.062 / Rsym value: 0.053 / Net I/av σ(I): 8.1 / Net I/σ(I): 16 / Num. measured all: 285097
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
1.45-1.536.60.2962.54059061280.1350.3510.2965.199.1
1.53-1.626.70.1983.83838857400.090.2360.1986.898.3
1.62-1.736.80.1435.23734054750.0640.1690.1439.199.7
1.73-1.876.60.0997.43305750390.0450.1180.09911.998.3
1.87-2.056.90.0719.83283847250.0320.0850.07116.999.9
2.05-2.296.80.05612.12883642590.0250.0670.05621.499.7
2.29-2.656.90.0513.42592137470.0220.0590.0524.899
2.65-3.246.80.04514.42198232120.020.0530.04529.999.6
3.24-4.596.80.04115.41695924890.0170.0460.04135.699.4
4.59-69.2856.60.03716.6918613980.0160.0420.03734.399.3

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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: 1.45→69.28 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2062 4219 10 %RANDOM
Rwork0.1722 ---
obs0.1756 37979 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 60.91 Å2 / Biso mean: 18.753 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20.1 Å2
2---0.44 Å2-0 Å2
3---0.6 Å2
Refinement stepCycle: final / Resolution: 1.45→69.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 52 261 2349
Biso mean--19.3 30 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122231
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.6713053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2925273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.72723.211109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38115355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.606159
X-RAY DIFFRACTIONr_chiral_restr0.1330.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.021767
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 307 -
Rwork0.214 2793 -
all-3100 -
obs--99.52 %

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