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- PDB-8fal: Masking thiol reactivity with thioamide-based MBPs- carbonic anhy... -

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Basic information

Entry
Database: PDB / ID: 8fal
TitleMasking thiol reactivity with thioamide-based MBPs- carbonic anhydrase II complexed with benzo[d]thiazole-2(3H)-thione
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Human Carbonic anhydrases / matrix metalloproteinases / metal binding pharmacophore / fragment based drug discovery
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 / 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
MERCURIBENZOIC ACID / 1,3-benzothiazole-2(3H)-thione / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsKohlbrand, A.J. / Seo, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI149444 United States
CitationJournal: Chem.Commun.(Camb.) / Year: 2023
Title: Masking thiol reactivity with thioamide, thiourea, and thiocarbamate-based MBPs.
Authors: Seo, H. / Kohlbrand, A.J. / Stokes, R.W. / Chung, J. / Cohen, S.M.
History
DepositionNov 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Structure summary / Category: chem_comp / chem_comp_atom / chem_comp_bond / Item: _chem_comp.pdbx_synonyms

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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)29,9225
Polymers29,2891
Non-polymers6324
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.009, 41.143, 71.915
Angle α, β, γ (deg.)90.000, 104.556, 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

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Protein , 1 types, 1 molecules A

#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: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 311 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-XO9 / 1,3-benzothiazole-2(3H)-thione / 2-mercaptobenzothiazole, thione tautomer


Mass: 167.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NS2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MBO / MERCURIBENZOIC ACID


Mass: 321.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5HgO2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / 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: 2.08 Å3/Da / Density % sol: 40.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.6-3.0 M Ammonium sulfate in 50 mM Tris-Sulfate (pH 8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: APEX II CCD / Detector: CCD / Date: Jun 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.37→35.42 Å / Num. obs: 88780 / % possible obs: 99 % / Redundancy: 4 % / Biso Wilson estimate: 11.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11
Reflection shellResolution: 1.37→1.42 Å / Num. unique obs: 2136 / CC1/2: 0.335

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
APEXdata reduction
APEXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→35.42 Å / SU ML: 0.1489 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2672
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 3769 4.25 %
Rwork0.1897 85011 -
obs0.1911 88780 90.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.02 Å2
Refinement stepCycle: LAST / Resolution: 1.37→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 25 307 2374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212139
X-RAY DIFFRACTIONf_angle_d1.23662904
X-RAY DIFFRACTIONf_chiral_restr0.0978300
X-RAY DIFFRACTIONf_plane_restr0.0097375
X-RAY DIFFRACTIONf_dihedral_angle_d6.495275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.390.4497110.3291X-RAY DIFFRACTION8.53
1.39-1.410.3425390.2703978X-RAY DIFFRACTION27.88
1.41-1.430.2729750.271672X-RAY DIFFRACTION48.95
1.43-1.450.27291390.26062717X-RAY DIFFRACTION78.72
1.45-1.470.2631460.2493403X-RAY DIFFRACTION96.78
1.47-1.490.24441270.23893376X-RAY DIFFRACTION97.52
1.49-1.520.2731820.23653391X-RAY DIFFRACTION98.08
1.52-1.540.25871260.23953428X-RAY DIFFRACTION99.05
1.54-1.570.27541570.22713443X-RAY DIFFRACTION99.39
1.57-1.60.24391730.22073453X-RAY DIFFRACTION99.78
1.6-1.630.23981420.21383498X-RAY DIFFRACTION99.81
1.63-1.670.26051490.21643454X-RAY DIFFRACTION99.89
1.67-1.710.261570.21553458X-RAY DIFFRACTION99.92
1.71-1.750.20741530.20573445X-RAY DIFFRACTION99.89
1.75-1.80.22931580.2013539X-RAY DIFFRACTION99.89
1.8-1.850.2041430.19473383X-RAY DIFFRACTION99.97
1.85-1.910.24541700.18873479X-RAY DIFFRACTION99.89
1.91-1.980.21321430.18753458X-RAY DIFFRACTION99.92
1.98-2.060.24721700.18183471X-RAY DIFFRACTION99.97
2.06-2.150.19771360.17693437X-RAY DIFFRACTION99.97
2.15-2.260.20911620.17523491X-RAY DIFFRACTION99.92
2.26-2.410.21971450.17213479X-RAY DIFFRACTION99.83
2.41-2.590.24881600.18533437X-RAY DIFFRACTION99.86
2.59-2.850.20491530.1883446X-RAY DIFFRACTION99.7
2.85-3.260.20081500.17933499X-RAY DIFFRACTION99.67
3.26-4.110.19231480.1543437X-RAY DIFFRACTION99.47
4.11-35.420.20521550.18073448X-RAY DIFFRACTION99.5
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.84171005722-0.423720444379-0.2975339062640.849615511204-0.3132372552681.90566505964-0.1623780644370.251316168203-0.336902680695-0.175997345285-0.19326033829-0.4044183238710.2483501159670.188286996861-0.06473794721220.05697949096680.004614229883220.1227508551930.1875265867540.007359011447340.3521180567729.765612541-4.4543092556914.5148527352
22.52968179150.152813416861-0.4261738288891.437184566230.3554811255291.09636733932-0.144524312225-0.2427665925520.06688535472210.3407124552330.161107666365-0.1948948806110.04925486443870.1336458628440.03811824438670.08325052948310.043778679593-0.03690743958150.135349412532-0.01378298005220.097981559016217.9390849386-3.7027998605528.9802010959
30.667387426286-0.7600314952860.8000064982281.65406605339-0.4325160853711.6687226816-0.00568888217356-0.2244851622310.0257161155363-0.1852039176730.07927995547820.174687975489-0.323205260286-0.199079984848-0.07966849195010.2019888459080.00524938486555-0.01412764841920.1353836863330.003416934780840.09296760553665.807446072073.1649443496714.0533432298
41.10294276855-0.496497969964-0.1738666542322.72788468774-0.02658167520391.3720388439-0.0305718835737-0.05868316154410.0248265251943-0.1045787377560.05904670282410.132591499124-0.0690013176243-0.0205125587949-0.02962409610840.0310682921675-0.011055558301-0.01720461330320.0657888511596-0.0004835063299070.04353323560868.35750387809-1.1077533577817.108836197
51.102747295670.5745946326670.2403501986614.174457002421.241741012321.79689160911-0.0061687015455-0.05392281395780.0889437148455-0.123906183330.004551469916980.110815038437-0.149059256090.0772438417561-0.004247216918760.0362307422037-3.11386405158E-5-0.005876647801540.0701785572245-3.06545868545E-50.0300473799919.397202138834.0830924714317.9562476039
66.721415028522.24243071326-3.795072529872.0322063657-1.589702061133.32855796325-0.0918553690330.528672828896-0.129543547894-0.6019250494230.03031371774520.1386542540440.0113421627126-0.344481515124-0.01478279913130.3423877944030.0244552991349-0.1135346629670.111251802225-0.02574988523040.05791973550785.4492939484-6.421724396540.184700215581
70.555453115058-0.290703474490.04161770889061.351640848570.3176894806020.937820946161-0.0061749573649-0.00794807195906-0.00957293413669-0.2530122874880.02330038535650.125876470138-0.0733058033878-0.0278105576649-0.03271027557570.09414559091210.00321404160321-0.02423295911810.06948261709660.009233500334240.0610329252557.87857523739-1.6310510423215.5431165829
84.603673918540.418644566116-2.033790785651.26493730293-1.244033112392.02719580087-0.002730067301150.285643341582-0.0804272700879-0.5545651913690.034280035103-0.115474248358-0.1323334472870.0985454445455-0.01554276902520.266533347906-0.03834302851070.04938217478330.113256920183-0.03423886969130.084461120953316.4713630596-10.98296376990.869707527925
92.03830641091-0.483930104483-0.6402437028571.977598535731.325498440052.45888944901-0.0209751756629-0.3045748815750.002512040018870.1180911491310.255724193936-0.150303358692-0.03809108565970.153435208425-0.1913393517030.0705064932830.0191057316270.0003752120191770.09109803497460.03337908556730.061191902043815.6677014423-6.6521170243223.6125261945
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 19 )4 - 191 - 16
22chain 'A' and (resid 20 through 39 )20 - 3917 - 36
33chain 'A' and (resid 40 through 70 )40 - 7037 - 67
44chain 'A' and (resid 71 through 115 )71 - 11568 - 112
55chain 'A' and (resid 116 through 154 )116 - 154113 - 150
66chain 'A' and (resid 155 through 167 )155 - 167151 - 163
77chain 'A' and (resid 168 through 219 )168 - 219164 - 215
88chain 'A' and (resid 220 through 238 )220 - 238216 - 234
99chain 'A' and (resid 239 through 261 )239 - 261235 - 257

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