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- PDB-5ogo: Crystal structure of chimeric carbonic anhydrase I with 3-(Benzyl... -

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Basic information

Entry
Database: PDB / ID: 5ogo
TitleCrystal structure of chimeric carbonic anhydrase I with 3-(Benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex / double binding
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 / angiotensin-activated signaling pathway ...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 / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / morphogenesis of an epithelium / 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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-WWO / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 0.99 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: To be published
Title: Crystal structure of chimeric carbonic anhydrase I with 3-(Benzylamino)-2,5,6-trifluoro-4-[(2-hydroxyethyl)sulfonyl]benzenesulfonamide
Authors: Smirnov, A. / Manakova, E. / Grazulis, S. / Matulis, D.
History
DepositionJul 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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)31,04111
Polymers29,3291
Non-polymers1,71210
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1630 Å2
ΔGint11 kcal/mol
Surface area11930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.094, 41.426, 71.654
Angle α, β, γ (deg.)90.000, 104.350, 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: 29329.086 Da / Num. of mol.: 1 / Fragment: chimeric carbonic anhydrase I
Mutation: N62V, N67H, I91F, V121A, F130L, V134A, T199H, L203Y
Source method: isolated from a genetically manipulated source
Details: The active site of human carbonic anhydrase I in carbonic anhydrase II was reconstructed by means of eight point mutations: N62V, N67H, I91F, V121A, F130L, V134A, T199H, and L203Y.
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 , 7 types, 343 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 424.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15F3N2O5S2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 163.172 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.06 Å3/Da / Density % sol: 40.4 % / Mosaicity: 0 °
Crystal growTemperature: 291 K / Method: evaporation / pH: 7
Details: Crystallization buffer: 0.1M sodium bicine (pH 9.0), 0.2M ammonium sulfate and 2M sodium malonate (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 0.988→41.426 Å / Num. all: 128596 / Num. obs: 128596 / % possible obs: 96.4 % / Redundancy: 3.2 % / Rpim(I) all: 0.03 / Rrim(I) all: 0.056 / Rsym value: 0.039 / Net I/av σ(I): 4.107 / Net I/σ(I): 14.1 / Num. measured all: 410103
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
0.99-1.042.80.2622.90.2040.3530.26285
1.04-1.1130.164.80.1230.2160.1696.2
1.11-1.183.10.1027.40.0780.140.10298.3
1.18-1.283.20.0779.70.0610.110.07797.9
1.28-1.43.40.05912.10.0470.0870.05999
1.4-1.563.30.04515.30.0370.0690.04598.5
1.56-1.83.50.03518.40.0290.0550.03599.4
1.8-2.213.30.0320.10.0240.0450.0398.7
2.21-3.133.50.02720.50.0220.0410.02799.7
3.13-41.4263.40.049.20.0290.0540.0499.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMACrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HT0

4ht0


Resolution: 0.99→39.72 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / SU R Cruickshank DPI: 0.0225 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.024
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1484 12806 10 %RANDOM
Rwork0.1244 ---
obs0.1268 115769 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 151.12 Å2 / Biso mean: 14.434 Å2 / Biso min: 4.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20.14 Å2
2---0.09 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 0.99→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 0 134 333 2530
Biso mean--25.67 25.41 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.022518
X-RAY DIFFRACTIONr_angle_refined_deg2.8342.0033451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.49824.587109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18315400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.951158
X-RAY DIFFRACTIONr_chiral_restr0.2680.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211989
X-RAY DIFFRACTIONr_rigid_bond_restr9.46432518
X-RAY DIFFRACTIONr_sphericity_free22.9985334
X-RAY DIFFRACTIONr_sphericity_bonded14.12652427
LS refinement shellResolution: 0.988→1.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.196 679 -
Rwork0.183 6435 -
all-7114 -
obs--72.61 %

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