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- PDB-8ogd: Structure of zinc(II) double mutant human carbonic anhydrase II b... -

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Basic information

Entry
Database: PDB / ID: 8ogd
TitleStructure of zinc(II) double mutant human carbonic anhydrase II bound to thiocyanate
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Inhibitor / thiocyanate / zinc
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 / morphogenesis of an epithelium / 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 / one-carbon metabolic process / apical part of cell / myelin sheath / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
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
4-(HYDROXYMERCURY)BENZOIC ACID / THIOCYANATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSilva, J.M. / Cerofolini, L. / Carvalho, A.L. / Ravera, E. / Fragai, M. / Parigi, G. / Macedo, A.L. / Geraldes, C.F.G.C. / Luchinat, C.
Funding support Italy, Portugal, 11items
OrganizationGrant numberCountry
Other government
Florence Instruct-ERIC Center Italy
Fundacao para a Ciencia e a TecnologiaUIDP/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/04378/2020 Portugal
Fundacao para a Ciencia e a TecnologiaLA/P/0140/2020 Portugal
Fundacao para a Ciencia e a TecnologiaPD/BD/135180/2017 Portugal
Fundacao para a Ciencia e a TecnologiaPD/00065/2013 Portugal
Fundacao para a Ciencia e a TecnologiaRECI/BBB-BEP/0124/2012 Portugal
Fundacao para a Ciencia e a TecnologiaROTEIRO/0031/2013PINFRA/22161/2016 Portugal
Fundacao para a Ciencia e a TecnologiaUIDB/00313/2020 Portugal
Fundacao para a Ciencia e a TecnologiaUIDP/00313/2020 Portugal
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase.
Authors: Silva, J.M. / Cerofolini, L. / Carvalho, A.L. / Ravera, E. / Fragai, M. / Parigi, G. / Macedo, A.L. / Geraldes, C.F.G.C. / Luchinat, C.
History
DepositionMar 20, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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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)29,7034
Polymers29,2411
Non-polymers4623
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, The protein elutes from the column at an expected volume for a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-43 kcal/mol
Surface area11570 Å2
Unit cell
Length a, b, c (Å)42.028, 41.333, 72.250
Angle α, β, γ (deg.)90.000, 104.427, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29240.973 Da / Num. of mol.: 1 / Mutation: H3N and H4N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase
#2: Chemical ChemComp-HGB / 4-(HYDROXYMERCURY)BENZOIC ACID


Mass: 338.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6HgO3
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 40.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, 2.9 M ammonium sulfate, 1 mM 4-hydroxymercuric benzoic acid sodium salt.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→23.77 Å / Num. obs: 24493 / % possible obs: 99.84 % / Redundancy: 1.9 % / Biso Wilson estimate: 10.89 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.44
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 2410 / CC1/2: 0.659

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
carelessdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→23.77 Å / SU ML: 0.1661 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.4287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1981 1160 4.74 %
Rwork0.1713 23308 -
obs0.1725 24468 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.98 Å2
Refinement stepCycle: LAST / Resolution: 1.75→23.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 14 362 2423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01082164
X-RAY DIFFRACTIONf_angle_d1.56782936
X-RAY DIFFRACTIONf_chiral_restr0.0721305
X-RAY DIFFRACTIONf_plane_restr0.0108382
X-RAY DIFFRACTIONf_dihedral_angle_d6.475278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.830.30721260.2652885X-RAY DIFFRACTION99.77
1.83-1.930.28611450.22822900X-RAY DIFFRACTION99.87
1.93-2.050.23711350.19862893X-RAY DIFFRACTION99.84
2.05-2.20.21361690.16722870X-RAY DIFFRACTION99.87
2.2-2.430.17411320.15762935X-RAY DIFFRACTION99.93
2.43-2.780.17661430.16282915X-RAY DIFFRACTION100
2.78-3.50.18081610.15572916X-RAY DIFFRACTION100
3.5-23.770.16081490.14412994X-RAY DIFFRACTION99.87

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