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- PDB-8oge: Structure of cobalt(II) substituted double mutant human carbonic ... -

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Basic information

Entry
Database: PDB / ID: 8oge
TitleStructure of cobalt(II) substituted double mutant human carbonic anhydrase II bound to thiocyanate
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / Inhibitor / thiocyanate / cobalt
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 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 Italy
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/BBBBEP/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)29,6974
Polymers29,2411
Non-polymers4563
Water5,278293
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration results are consistent with a monomer in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-17 kcal/mol
Surface area11630 Å2
Unit cell
Length a, b, c (Å)42.185, 41.343, 72.530
Angle α, β, γ (deg.)90.000, 104.470, 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, 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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, 2.9 M Ammonium Sulfate, 1 mM 4-hidroxymercuric benzoic acid sodium salt

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.608 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.608 Å / Relative weight: 1
ReflectionResolution: 1.46→40.85 Å / Num. obs: 60302 / % possible obs: 84.11 % / Redundancy: 2.9 % / Biso Wilson estimate: 13.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Net I/σ(I): 22.87
Reflection shellResolution: 1.46→1.52 Å / Rmerge(I) obs: 0.136 / Num. unique obs: 749 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
TRUNCATEdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→40.85 Å / SU ML: 0.1051 / Cross valid method: FREE R-VALUE / σ(F): 1.45 / Phase error: 17.9617
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1623 3156 5.23 %
Rwork0.1349 57146 -
obs0.1364 60302 73.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.78 Å2
Refinement stepCycle: LAST / Resolution: 1.46→40.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 14 293 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02242164
X-RAY DIFFRACTIONf_angle_d2.03642936
X-RAY DIFFRACTIONf_chiral_restr0.1334305
X-RAY DIFFRACTIONf_plane_restr0.0174382
X-RAY DIFFRACTIONf_dihedral_angle_d6.4397278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.490.3365100.2665176X-RAY DIFFRACTION5.25
1.49-1.510.2259290.2004474X-RAY DIFFRACTION13.95
1.51-1.530.2432330.164805X-RAY DIFFRACTION24.28
1.53-1.560.1868620.16161232X-RAY DIFFRACTION36.14
1.56-1.590.1954800.15011644X-RAY DIFFRACTION48.39
1.59-1.620.15791100.15412147X-RAY DIFFRACTION63.9
1.62-1.650.19121370.14492731X-RAY DIFFRACTION80.25
1.65-1.690.19732000.14332918X-RAY DIFFRACTION86.56
1.69-1.730.17511590.14082909X-RAY DIFFRACTION87.58
1.73-1.770.17071400.13862967X-RAY DIFFRACTION86.93
1.77-1.820.19211600.13762916X-RAY DIFFRACTION87.09
1.82-1.870.18041740.13722971X-RAY DIFFRACTION88.34
1.87-1.930.16891600.13372937X-RAY DIFFRACTION87.71
1.93-20.14121590.12852949X-RAY DIFFRACTION87.62
2-2.080.15611590.12793006X-RAY DIFFRACTION88.19
2.08-2.180.14211790.12483001X-RAY DIFFRACTION89.38
2.18-2.290.16641480.1323013X-RAY DIFFRACTION88.99
2.29-2.430.16831870.13112992X-RAY DIFFRACTION88.95
2.43-2.620.17751570.14093060X-RAY DIFFRACTION91.08
2.62-2.890.18491310.14093115X-RAY DIFFRACTION91.93
2.89-3.30.14791840.14023030X-RAY DIFFRACTION90.66
3.3-4.160.15422060.12013075X-RAY DIFFRACTION91.65
4.16-40.850.15091920.13853078X-RAY DIFFRACTION92.01
Refinement TLS params.Method: refined / Origin x: -30.5703056359 Å / Origin y: -1.76231123386 Å / Origin z: 16.2637377871 Å
111213212223313233
T0.0641160030041 Å2-0.00294689813383 Å2-0.00218728972096 Å2-0.0569242629533 Å20.0106346807776 Å2--0.077181067828 Å2
L0.822615723473 °2-0.149119195342 °20.0518517953723 °2-0.871760895811 °20.132898438683 °2--1.27340909519 °2
S-0.0129508555077 Å °-0.0202000148274 Å °0.035274251591 Å °-0.0356800350545 Å °0.00969005113369 Å °0.0136604542871 Å °-0.010071503453 Å °0.00233161801008 Å °0.00210510356593 Å °
Refinement TLS groupSelection details: all

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