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

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Basic information

Entry
Database: PDB / ID: 7nzx
TitleCrystal structure of chimeric carbonic anhydrase VA with 2,3,5,6-tetrafluoro-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 / 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-V13 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 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)30,0446
Polymers29,3771
Non-polymers6675
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-1 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.159, 41.334, 71.548
Angle α, β, γ (deg.)90.000, 104.130, 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 , 6 types, 305 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-V13 / 2,3,5,6-tetrafluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide


Mass: 337.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7F4NO5S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 40.23 %
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: 1.328→69.384 Å / Num. all: 53846 / Num. obs: 53846 / % possible obs: 97.3 % / Redundancy: 6.6 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Rsym value: 0.046 / Net I/av σ(I): 6 / Net I/σ(I): 20.4 / Num. measured all: 357152
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
1.33-1.45.70.2173.43920368720.1070.2630.2176.585.6
1.4-1.486.80.1644.55100475060.0740.1960.1649.199.2
1.48-1.596.60.1126.44664471110.0530.1370.1121299.2
1.59-1.716.90.0848.44562766210.0390.1040.08415.999.4
1.71-1.886.60.06310.84005260880.030.0780.06320.299.2
1.88-2.170.04713.83867755380.0220.0590.04727.599.6
2.1-2.426.70.04115.23254148700.020.0510.04131.999.2
2.42-2.977.10.03815.82950941770.0170.0470.03836.799.8
2.97-4.26.70.03813.42182032410.0170.0450.0384199.3
4.2-69.3846.60.04310.51207518220.020.0510.04341.699.4

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 1.33→69.38 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 5334 9.9 %RANDOM
Rwork0.1242 ---
obs0.1288 48495 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 117.79 Å2 / Biso mean: 19.694 Å2 / Biso min: 7.37 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å2-0.14 Å2
2--0.33 Å20 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 1.33→69.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 57 300 2406
Biso mean--29.17 32.95 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122267
X-RAY DIFFRACTIONr_angle_refined_deg2.3321.6663108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9715279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52423.874111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.989157
X-RAY DIFFRACTIONr_chiral_restr0.1580.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021799
X-RAY DIFFRACTIONr_rigid_bond_restr7.25532267
X-RAY DIFFRACTIONr_sphericity_free26.9045175
X-RAY DIFFRACTIONr_sphericity_bonded16.59852321
LS refinement shellResolution: 1.33→1.363 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.204 336 -
Rwork0.147 2683 -
obs--73.76 %

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