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- PDB-6skt: Crystal structure of bovine carbonic anhydrase II in complex with... -

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Basic information

Entry
Database: PDB / ID: 6skt
TitleCrystal structure of bovine carbonic anhydrase II in complex with a benzenesulfonamide-based ligand (SH0)
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CARBONIC ANHYDRASE II / CA2 / SULFONAMIDE / COMPLEX
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process / apical part of cell / zinc ion binding / plasma membrane / 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
COPPER (II) ION / Chem-E6B / Carbonic anhydrase 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGroves, M.R. / Wang, W. / van Oosterwijk, N.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research722.012.003 Netherlands
CitationJournal: To Be Published
Title: Target diazotransfer reagents to label metalloenzymes
Authors: Groves, M.R. / Wang, W. / van Oosterwijk, N. / Witte, M. / Lohse, J.
History
DepositionAug 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 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)29,7316
Polymers29,1521
Non-polymers5795
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area550 Å2
ΔGint-27 kcal/mol
Surface area11510 Å2
Unit cell
Length a, b, c (Å)67.619, 67.619, 123.429
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1248-

HOH

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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 II / CA-II


Mass: 29151.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Blood / References: UniProt: P00921, carbonic anhydrase

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Non-polymers , 5 types, 180 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: 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
#5: Chemical ChemComp-E6B / ~{N}-[2-(1~{H}-imidazol-4-yl)ethyl]-4-sulfamoyl-benzamide


Mass: 294.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O3S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.82 Å3/Da / Density meas: 56.24 Mg/m3 / Density % sol: 56.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH7.5, 14% PEG3350, 20% Glycerol, 5mM CuCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2017 / Details: Double crystal monochromator
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.9→42.4 Å / Num. obs: 26439 / % possible obs: 99.9 % / Redundancy: 19.6 % / Biso Wilson estimate: 33.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05175 / Rpim(I) all: 0.01206 / Rrim(I) all: 0.05318 / Net I/σ(I): 35.99
Reflection shellResolution: 1.9→1.96 Å / Redundancy: 20.1 % / Rmerge(I) obs: 0.2529 / Mean I/σ(I) obs: 8.65 / Num. unique obs: 2581 / CC1/2: 0.994 / Rpim(I) all: 0.05758 / Rrim(I) all: 0.2595 / % possible all: 99.81

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
XDS20170601data reduction
PHASER5.8.0189phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V9E

1v9e


Resolution: 1.9→42.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.763 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.118
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 1333 5 %RANDOM
Rwork0.1771 ---
obs0.1784 25192 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.96 Å2 / Biso mean: 38.411 Å2 / Biso min: 26.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.46 Å20 Å2
2--0.91 Å20 Å2
3----2.97 Å2
Refinement stepCycle: final / Resolution: 1.9→42.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 29 175 2252
Biso mean--44.98 47.36 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192136
X-RAY DIFFRACTIONr_bond_other_d0.0020.021908
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9372906
X-RAY DIFFRACTIONr_angle_other_deg0.9462.9934447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9135257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.07424.412102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70915334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.207159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212373
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02433
LS refinement shellResolution: 1.9→1.947 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.241 93 -
Rwork0.217 1808 -
obs--99.01 %
Refinement TLS params.Method: refined / Origin x: 14.3151 Å / Origin y: 72.6452 Å / Origin z: 126.5968 Å
111213212223313233
T0.0976 Å20.116 Å20.0245 Å2-0.375 Å20.0572 Å2--0.0836 Å2
L0.1625 °20.0188 °20.0371 °2-0.455 °2-0.1414 °2--0.9997 °2
S0.0704 Å °0.0231 Å °0.0831 Å °0.004 Å °0.0021 Å °-0.0918 Å °0.1433 Å °-0.1899 Å °-0.0725 Å °

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