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

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Basic information

Entry
Database: PDB / ID: 6sks
TitleCrystal structure of bovine carbonic anhydrase II in complex with a benzenesulfonamide-based ligand (SH1)
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 activity / cyanamide hydratase / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / apical part of cell ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase activity / cyanamide hydratase / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / 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-E68 / Carbonic anhydrase 2
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0079
Polymers29,1521
Non-polymers8558
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-46 kcal/mol
Surface area11640 Å2
Unit cell
Length a, b, c (Å)67.406, 67.406, 123.319
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-463-

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 (domestic cattle) / Tissue: Blood / References: UniProt: P00921, carbonic anhydrase

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Non-polymers , 5 types, 254 molecules

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


Mass: 63.546 Da / Num. of mol.: 4 / 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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-E68 / ~{N}-[2-[2-(1~{H}-imidazol-4-yl)ethylamino]-2-oxidanylidene-ethyl]-4-sulfamoyl-benzamide


Mass: 351.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H17N5O4S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
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: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 18, 2017 / Details: Double crystal Monochrom
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→43 Å / Num. obs: 33424 / % possible obs: 99.95 % / Redundancy: 19.7 % / Biso Wilson estimate: 26.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0813 / Rpim(I) all: 0.01886 / Rrim(I) all: 0.08351 / Net I/σ(I): 22.99
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 18.8 % / Rmerge(I) obs: 0.5583 / Num. unique obs: 3271 / CC1/2: 0.963 / Rpim(I) all: 0.1313 / Rrim(I) all: 0.5738 / Χ2: 4 / % possible all: 99.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDS20170601data reduction
Aimless0.5.32data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V9E

1v9e


Resolution: 1.75→42.3 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.129 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.094
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 1736 5.2 %RANDOM
Rwork0.1688 ---
obs0.1701 31827 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.93 Å2 / Biso mean: 30.944 Å2 / Biso min: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.46 Å2
Refinement stepCycle: final / Resolution: 1.75→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 41 246 2341
Biso mean--39.74 41.53 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192185
X-RAY DIFFRACTIONr_bond_other_d0.0020.021939
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.9332975
X-RAY DIFFRACTIONr_angle_other_deg0.9852.9914524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8695264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92824.245106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.395159
X-RAY DIFFRACTIONr_chiral_restr0.1060.2309
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212445
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02445
LS refinement shellResolution: 1.75→1.792 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.264 138 -
Rwork0.227 2270 -
obs--98.33 %
Refinement TLS params.Method: refined / Origin x: -19.417 Å / Origin y: 14.2358 Å / Origin z: 3.1354 Å
111213212223313233
T0.0812 Å20.0625 Å20.0149 Å2-0.2209 Å20.0478 Å2--0.0474 Å2
L0.2196 °2-0.0255 °2-0.0028 °2-0.3986 °2-0.0484 °2--0.7157 °2
S0.1057 Å °0.0285 Å °0.0396 Å °-0.0016 Å °-0.0508 Å °-0.1189 Å °0.0466 Å °-0.1985 Å °-0.0548 Å °

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