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- PDB-7q1c: Crystal structure of Trypanosoma cruzi histone deacetylase DAC2 c... -

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Basic information

Entry
Database: PDB / ID: 7q1c
TitleCrystal structure of Trypanosoma cruzi histone deacetylase DAC2 complexed with a hydroxamate inhibitor
ComponentsHistone deacetylase DAC2
KeywordsHYDROLASE / Epigenetics / Trypanosoma cruzi / Histone deacetylase / DAC2 / Pathogen
Function / homology: / (E)-3-dibenzofuran-4-yl-N-oxidanyl-prop-2-enamide
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRamos-Morales, E. / Marek, M. / Romier, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme602080European Union
Citation
Journal: Cell Rep / Year: 2021
Title: Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2.
Authors: Marek, M. / Ramos-Morales, E. / Picchi-Constante, G.F.A. / Bayer, T. / Norstrom, C. / Herp, D. / Sales-Junior, P.A. / Guerra-Slompo, E.P. / Hausmann, K. / Chakrabarti, A. / Shaik, T.B. / ...Authors: Marek, M. / Ramos-Morales, E. / Picchi-Constante, G.F.A. / Bayer, T. / Norstrom, C. / Herp, D. / Sales-Junior, P.A. / Guerra-Slompo, E.P. / Hausmann, K. / Chakrabarti, A. / Shaik, T.B. / Merz, A. / Troesch, E. / Schmidtkunz, K. / Goldenberg, S. / Pierce, R.J. / Mourao, M.M. / Jung, M. / Schultz, J. / Sippl, W. / Zanchin, N.I.T. / Romier, C.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionOct 18, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase DAC2
B: Histone deacetylase DAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,61110
Polymers100,8172
Non-polymers7948
Water4,143230
1
A: Histone deacetylase DAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8065
Polymers50,4091
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase DAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8065
Polymers50,4091
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.071, 95.353, 96.920
Angle α, β, γ (deg.)90.000, 103.501, 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 Histone deacetylase DAC2


Mass: 50408.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-T56 / (E)-3-dibenzofuran-4-yl-N-oxidanyl-prop-2-enamide


Mass: 253.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 7.5%(W/V) PEG 8K, 0.1 M Bis-tris pH 6.3, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.979957 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979957 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 52026 / % possible obs: 99.7 % / Redundancy: 7 % / Biso Wilson estimate: 36.15 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.195 / Net I/σ(I): 7.76
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 6.78 % / Rmerge(I) obs: 1.687 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 8289 / CC1/2: 0.425 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.19rc4_4035refinement
PHENIX1.19rc4_4035refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T67

1t67


Resolution: 2.3→48.11 Å / SU ML: 0.3138 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 27.335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2243 5163 5.06 %
Rwork0.1964 96927 -
obs0.1979 51399 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.52 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 44 230 6739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00746668
X-RAY DIFFRACTIONf_angle_d0.92739055
X-RAY DIFFRACTIONf_chiral_restr0.0541023
X-RAY DIFFRACTIONf_plane_restr0.00711170
X-RAY DIFFRACTIONf_dihedral_angle_d13.55312403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.320.36671550.32583122X-RAY DIFFRACTION95.57
2.32-2.350.30941750.30753227X-RAY DIFFRACTION100
2.35-2.380.27941930.30583187X-RAY DIFFRACTION99.85
2.38-2.410.33481740.30593215X-RAY DIFFRACTION99.97
2.41-2.440.31451310.30553330X-RAY DIFFRACTION99.88
2.44-2.480.29462030.28893162X-RAY DIFFRACTION99.97
2.48-2.510.33981620.28343287X-RAY DIFFRACTION99.97
2.51-2.550.34181750.29413217X-RAY DIFFRACTION100
2.55-2.590.35761340.28373274X-RAY DIFFRACTION99.94
2.59-2.630.29251720.26813242X-RAY DIFFRACTION99.94
2.63-2.680.29911670.26733193X-RAY DIFFRACTION99.97
2.68-2.730.31811700.24693287X-RAY DIFFRACTION99.91
2.73-2.780.23621700.24483266X-RAY DIFFRACTION100
2.78-2.830.32371650.24083223X-RAY DIFFRACTION99.97
2.83-2.90.28111890.23043235X-RAY DIFFRACTION99.97
2.9-2.960.26041860.22613235X-RAY DIFFRACTION99.97
2.96-3.040.24631710.23813199X-RAY DIFFRACTION99.94
3.04-3.120.25811640.23553247X-RAY DIFFRACTION99.97
3.12-3.210.25971450.2173264X-RAY DIFFRACTION99.82
3.21-3.320.21821780.19393288X-RAY DIFFRACTION99.97
3.32-3.430.21121290.19093230X-RAY DIFFRACTION99.94
3.43-3.570.18931990.17933209X-RAY DIFFRACTION99.97
3.57-3.730.21942040.1743234X-RAY DIFFRACTION99.94
3.73-3.930.1921660.15543241X-RAY DIFFRACTION99.85
3.93-4.180.16482160.14583157X-RAY DIFFRACTION99.62
4.18-4.50.19021740.13193215X-RAY DIFFRACTION99.68
4.5-4.950.13341780.12423239X-RAY DIFFRACTION99.94
4.95-5.660.18041700.15263242X-RAY DIFFRACTION99.88
5.67-7.130.18691810.16883215X-RAY DIFFRACTION99.79
7.14-48.110.19831670.15523245X-RAY DIFFRACTION99.59
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)
10.3740776626450.09566693923574.87580686622E-50.4199329765030.269459616220.922938666892-0.02419709414660.019897995144-0.016796174661-0.0123381982905-0.03492349385960.0263577594258-0.0709708863955-0.122480187943-9.93700699027E-60.2662056493390.0206170300177-0.01638065309410.278042610179-0.003739669259430.29870131649687.7211525303-91.32600964051.08713961395
20.3477763067750.155320054721-0.225384761080.698702496214-0.3586629924741.01030631512-0.0279633983291-0.0384288195471-0.0108309310606-0.0384987950927-0.0759346425984-0.0577963120483-0.01663024215810.1430627021864.14368519721E-60.249297219362-0.00882919465675-0.0001304833286550.2902391303410.02449284453670.28120528405153.9580487935-92.9589435607-40.9190052097
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 13 - 700 / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11chain AAA - E
22chain BBF - J

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