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- PDB-6syb: Crystal structure of carbonic anhydrase 2 with (3aR,4S,9bS)-4-(2-... -

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Entry
Database: PDB / ID: 6syb
TitleCrystal structure of carbonic anhydrase 2 with (3aR,4S,9bS)-4-(2-chloro-4-hydroxyphenyl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide
ComponentsCarbonic anhydrase 2
KeywordsLYASE / inhibitor / carbonic anhydrase 2 / sulfonamide
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, 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-LYQ / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAngeli, A. / Ferraroni, M.
CitationJournal: To Be Published
Title: Crystal structure of carbonic anhydrase 2 with (3aR,4S,9bS)-4-(2-chloro-4-hydroxyphenyl)-3a,4,5,9b-tetrahydro-3H-cyclopenta[c]quinoline-8-sulfonamide
Authors: Angeli, A. / Ferraroni, M.
History
DepositionSep 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8254
Polymers29,2891
Non-polymers5363
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area310 Å2
ΔGint-7 kcal/mol
Surface area11590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.290, 41.305, 71.935
Angle α, β, γ (deg.)90.000, 104.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LYQ / (3~{a}~{R},4~{S},9~{b}~{S})-4-(2-chloranyl-4-oxidanyl-phenyl)-2,3,3~{a},4,5,9~{b}-hexahydro-1~{H}-cyclopenta[c]quinoline-8-sulfonamide


Mass: 378.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H19ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5 M sodium citrate, 50 mM Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→69.68 Å / Num. obs: 31710 / % possible obs: 98.8 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.037 / Rrim(I) all: 0.122 / Net I/σ(I): 10.8 / Num. measured all: 307450 / Scaling rejects: 6411
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.6-1.635.90.912840614320.6750.4030.9991.692
8.75-69.689.80.03521892230.9990.0110.03625.599.7

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FIK

4fik


Resolution: 1.6→69.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.28 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.098
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 1544 4.9 %RANDOM
Rwork0.1736 ---
obs0.1756 30125 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 51.12 Å2 / Biso mean: 15.799 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å2-0.07 Å2
2---0.6 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.6→69.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 32 182 2265
Biso mean--26.19 24.51 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132194
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171972
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.6352995
X-RAY DIFFRACTIONr_angle_other_deg1.3981.5924615
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6065272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09123.761109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25715358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.385157
X-RAY DIFFRACTIONr_chiral_restr0.0850.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
LS refinement shellResolution: 1.6→1.64 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.323 97 -
Rwork0.287 2093 -
obs--93.23 %

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