[English] 日本語
Yorodumi
- PDB-6htg: Crystal structure of Schistosoma mansoni HDAC8 complexed with a b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6htg
TitleCrystal structure of Schistosoma mansoni HDAC8 complexed with a benzohydroxamate inhibitor 4
ComponentsHistone deacetylase
KeywordsHYDROLASE / Epigenetics / Histone deacetylase / HDAC8 / Selective inhibitor / Pathogen
Function / homology
Function and homology information


histone deacetylase / histone deacetylase activity / negative regulation of transcription by RNA polymerase II / nucleus / metal ion binding
Similarity search - Function
Histone deacetylase domain / Arginase; Chain A / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIMETHYLFORMAMIDE / : / 3-benzamido-4-chloranyl-~{N}-oxidanyl-benzamide / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.939 Å
AuthorsShaik, T.B. / Marek, M. / Romier, C.
Funding support France, 2items
OrganizationGrant numberCountry
European Commission241865 France
European Commission602080 France
CitationJournal: J. Med. Chem. / Year: 2018
Title: Characterization of Histone Deacetylase 8 (HDAC8) Selective Inhibition Reveals Specific Active Site Structural and Functional Determinants.
Authors: Marek, M. / Shaik, T.B. / Heimburg, T. / Chakrabarti, A. / Lancelot, J. / Ramos-Morales, E. / Da Veiga, C. / Kalinin, D. / Melesina, J. / Robaa, D. / Schmidtkunz, K. / Suzuki, T. / Holl, R. ...Authors: Marek, M. / Shaik, T.B. / Heimburg, T. / Chakrabarti, A. / Lancelot, J. / Ramos-Morales, E. / Da Veiga, C. / Kalinin, D. / Melesina, J. / Robaa, D. / Schmidtkunz, K. / Suzuki, T. / Holl, R. / Ennifar, E. / Pierce, R.J. / Jung, M. / Sippl, W. / Romier, C.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 28, 2018Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase
B: Histone deacetylase
C: Histone deacetylase
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,35750
Polymers202,3324
Non-polymers4,02546
Water13,655758
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54812
Polymers50,5831
Non-polymers96511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,78615
Polymers50,5831
Non-polymers1,20314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,54812
Polymers50,5831
Non-polymers96511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,47511
Polymers50,5831
Non-polymers89210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.660, 70.640, 98.330
Angle α, β, γ (deg.)77.73, 75.86, 85.63
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Histone deacetylase


Mass: 50583.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: Escherichia coli (E. coli) / References: UniProt: A5H660, histone deacetylase

-
Non-polymers , 6 types, 804 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-T61 / 3-benzamido-4-chloranyl-~{N}-oxidanyl-benzamide


Mass: 290.702 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H11ClN2O3
#5: Chemical...
ChemComp-DMF / DIMETHYLFORMAMIDE


Mass: 73.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H7NO
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 758 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NA,K L-TARTRATE, 21% (W/V) PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.006365 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.006365 Å / Relative weight: 1
ReflectionResolution: 1.939→49.25 Å / Num. obs: 127015 / % possible obs: 95.07 % / Redundancy: 3.6 % / CC1/2: 0.917 / Rmerge(I) obs: 0.2585 / Net I/σ(I): 3.44
Reflection shellResolution: 1.939→2.008 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 11790 / CC1/2: 0.732 / % possible all: 88.06

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BZ5

4bz5


Resolution: 1.939→49.248 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 20.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 6350 5 %
Rwork0.169 --
obs0.1713 127009 95.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.939→49.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13019 0 246 758 14023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113699
X-RAY DIFFRACTIONf_angle_d118606
X-RAY DIFFRACTIONf_dihedral_angle_d14.7728025
X-RAY DIFFRACTIONf_chiral_restr0.061978
X-RAY DIFFRACTIONf_plane_restr0.0072458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.939-1.96110.29441700.24543230X-RAY DIFFRACTION74
1.9611-1.98410.2652050.20283895X-RAY DIFFRACTION95
1.9841-2.00830.2462140.18454076X-RAY DIFFRACTION96
2.0083-2.03370.23192130.17854036X-RAY DIFFRACTION96
2.0337-2.06050.2342120.1774041X-RAY DIFFRACTION95
2.0605-2.08870.24732130.17754037X-RAY DIFFRACTION95
2.0887-2.11860.24722120.1734028X-RAY DIFFRACTION96
2.1186-2.15020.23892130.17194053X-RAY DIFFRACTION96
2.1502-2.18380.22162120.17474019X-RAY DIFFRACTION95
2.1838-2.21960.24222130.16564057X-RAY DIFFRACTION95
2.2196-2.25790.24242110.17164003X-RAY DIFFRACTION95
2.2579-2.29890.22432140.16624066X-RAY DIFFRACTION95
2.2989-2.34310.23132110.16644002X-RAY DIFFRACTION95
2.3431-2.3910.22272110.16864013X-RAY DIFFRACTION95
2.391-2.4430.2162120.16094022X-RAY DIFFRACTION95
2.443-2.49980.21282030.16853859X-RAY DIFFRACTION92
2.4998-2.56230.22482100.17653992X-RAY DIFFRACTION94
2.5623-2.63160.24812170.17484124X-RAY DIFFRACTION97
2.6316-2.7090.26042170.1764134X-RAY DIFFRACTION97
2.709-2.79640.21832150.16784072X-RAY DIFFRACTION97
2.7964-2.89640.20212160.17114110X-RAY DIFFRACTION97
2.8964-3.01230.23972150.17294083X-RAY DIFFRACTION97
3.0123-3.14940.20772150.17234086X-RAY DIFFRACTION96
3.1494-3.31540.21292140.17154072X-RAY DIFFRACTION96
3.3154-3.52310.19842130.1654036X-RAY DIFFRACTION95
3.5231-3.7950.20332090.15733979X-RAY DIFFRACTION95
3.795-4.17670.1822210.14984200X-RAY DIFFRACTION98
4.1767-4.78070.16512180.1444132X-RAY DIFFRACTION98
4.7807-6.02140.2042170.17334130X-RAY DIFFRACTION98
6.0214-49.26360.21832140.18934072X-RAY DIFFRACTION96
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)
10.59770.1407-0.17890.4668-0.22860.56490.0219-0.0802-0.02620.0422-0.0527-0.0182-0.0080.038-0.00050.0717-0.0057-0.00930.1311-0.00380.083153.579325.418185.9397
20.5644-0.15260.04430.4284-0.02540.33590.0108-0.04390.0044-0.0208-0.0315-0.0145-0.0066-0.005600.08890.0098-0.00650.11960.00410.11888.773343.082270.3406
30.2374-0.1584-0.02980.63750.12880.2555-0.0423-0.0231-0.0162-0.08330.03250.0091-0.0277-0.01710.00010.1111-0.001-0.00430.08210.00440.090444.7782.485840.758
40.49560.3253-0.13520.854-0.10910.4138-0.10870.0222-0.0727-0.11830.0584-0.06270.02430.0088-0.00280.1572-0.02210.01790.0851-0.01170.097365.128136.037825.0941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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