[English] 日本語
Yorodumi
- PDB-7q1b: Crystal structure of Trypanosoma cruzi histone deacetylase DAC2 c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q1b
TitleCrystal structure of Trypanosoma cruzi histone deacetylase DAC2 complexed with Quisinostat
ComponentsHistone deacetylase DAC2
KeywordsHYDROLASE / Epigenetics / Trypanosoma cruzi / Histone deacetylase / DAC2 / Pathogen
Function / homologyHistone deacetylase domain / Arginase; Chain A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-GOK / :
Function and homology information
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsMarek, M. / Ramos-Morales, E. / Romier, C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Communitys Seventh Framework Programme602080European Union
CitationJournal: 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.
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase DAC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0396
Polymers50,4091
Non-polymers6305
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint-1 kcal/mol
Surface area16320 Å2
Unit cell
Length a, b, c (Å)82.167, 93.584, 119.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase DAC2


Mass: 50408.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-GOK / 2-[4-[[(1-methylindol-3-yl)methylamino]methyl]piperidin-1-yl]-~{N}-oxidanyl-pyrimidine-5-carboxamide


Mass: 394.470 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H26N6O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antineoplastic, inhibitor*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 5%(W/V) PEG 6000, 0.1 M Hepes pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 50638 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 31.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.2
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 13 % / Rmerge(I) obs: 2.387 / Mean I/σ(I) obs: 1 / Num. unique obs: 8053 / CC1/2: 0.674

-
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: 1.75→46.79 Å / SU ML: 0.3232 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.8332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2182 4462 5 %
Rwork0.1923 84758 -
obs0.1936 46459 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 38 226 3301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613147
X-RAY DIFFRACTIONf_angle_d0.74314273
X-RAY DIFFRACTIONf_chiral_restr0.0492485
X-RAY DIFFRACTIONf_plane_restr0.0067570
X-RAY DIFFRACTIONf_dihedral_angle_d11.90651146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.61751410.57882686X-RAY DIFFRACTION96.52
1.77-1.790.53681520.51892873X-RAY DIFFRACTION99.54
1.79-1.810.52841450.48262769X-RAY DIFFRACTION99.49
1.81-1.840.41711550.39482877X-RAY DIFFRACTION99.44
1.84-1.860.31781430.3812768X-RAY DIFFRACTION99.39
1.86-1.890.35311500.34072801X-RAY DIFFRACTION99.56
1.89-1.910.37671500.31632884X-RAY DIFFRACTION99.87
1.91-1.940.3581430.28582769X-RAY DIFFRACTION99.66
1.94-1.970.3231470.26592843X-RAY DIFFRACTION99.67
1.97-2.010.28541510.25562860X-RAY DIFFRACTION99.8
2.01-2.040.29561460.23382811X-RAY DIFFRACTION100
2.04-2.080.2841480.24272829X-RAY DIFFRACTION99.93
2.08-2.120.26231470.22762814X-RAY DIFFRACTION99.93
2.12-2.160.24881550.22432864X-RAY DIFFRACTION99.83
2.16-2.210.25391450.22172831X-RAY DIFFRACTION99.93
2.21-2.260.25341490.22322838X-RAY DIFFRACTION100
2.26-2.320.22661510.1912796X-RAY DIFFRACTION100
2.32-2.380.19391450.18022850X-RAY DIFFRACTION100
2.38-2.450.21371490.19132823X-RAY DIFFRACTION99.93
2.45-2.530.19841520.19632832X-RAY DIFFRACTION99.93
2.53-2.620.21171470.17912835X-RAY DIFFRACTION99.97
2.62-2.720.23271520.18682840X-RAY DIFFRACTION99.87
2.72-2.850.24011500.18862827X-RAY DIFFRACTION99.93
2.85-30.2291440.192833X-RAY DIFFRACTION99.97
3-3.180.19521510.17462827X-RAY DIFFRACTION100
3.18-3.430.21811480.17862859X-RAY DIFFRACTION100
3.43-3.770.18141500.15982835X-RAY DIFFRACTION100
3.77-4.320.16581500.14382817X-RAY DIFFRACTION100
4.32-5.440.15481540.14092837X-RAY DIFFRACTION99.93
5.44-46.790.18671520.16652830X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 22.5271301061 Å / Origin y: 114.518105177 Å / Origin z: 16.0733411453 Å
111213212223313233
T0.271163438017 Å2-0.0174539709491 Å20.0298936721854 Å2-0.268722281699 Å2-0.0787182104011 Å2--0.259939798626 Å2
L1.46959474442 °20.313438341758 °20.268033150256 °2-0.860797880194 °2-0.0438993374518 °2--0.559017004457 °2
S-0.126949132578 Å °0.111227496219 Å °-0.263477401933 Å °-0.0356433002183 Å °0.0965287226999 Å °-0.0689381612475 Å °-0.0156371961578 Å °-0.0448314572825 Å °4.91180220153E-5 Å °
Refinement TLS groupSelection details: chain A

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more