[English] 日本語
Yorodumi
- PDB-7poz: Crystal structure of Schistosoma mansoni HDAC8 with DMSO bound in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7poz
TitleCrystal structure of Schistosoma mansoni HDAC8 with DMSO bound in the active site
ComponentsHistone deacetylase 8
KeywordsHYDROLASE / SmHDAC8 / histone-deacetilase / double-conformation
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 family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / histone deacetylase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSaccoccia, F. / Ruberti, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.
Authors: Saccoccia, F. / Pozzetti, L. / Gimmelli, R. / Butini, S. / Guidi, A. / Papoff, G. / Giannaccari, M. / Brogi, S. / Scognamiglio, V. / Gemma, S. / Ruberti, G. / Campiani, G.
History
DepositionSep 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
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 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1486
Polymers49,8341
Non-polymers3145
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-37 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.738, 70.738, 179.462
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase 8


Mass: 49834.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Gene: HDAC8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5H660

-
Non-polymers , 5 types, 190 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DMS / 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


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.25 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 21% PEG3350, 200mM Na/K-tartrate / Temp details: cold-room

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.73 Å / Num. obs: 34801 / % possible obs: 95.8 % / Redundancy: 4.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.049 / Rrim(I) all: 0.108 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.944.40.947981922410.6030.4961.0741.497.9
9.11-43.693.80.03813313500.9980.0210.04328.689.2

-
Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bz5

4bz5


Resolution: 1.9→43.73 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 6.934 / SU ML: 0.098 / SU R Cruickshank DPI: 0.1427 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1714 4.9 %RANDOM
Rwork0.1697 ---
obs0.1719 33072 94.34 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 145.55 Å2 / Biso mean: 31.397 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0 Å2
2---0.8 Å2-0 Å2
3---1.6 Å2
Refinement stepCycle: final / Resolution: 1.9→43.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 13 185 3442
Biso mean--31.14 36.63 -
Num. residues----405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133394
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173131
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.6344618
X-RAY DIFFRACTIONr_angle_other_deg1.2491.5757216
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9421.91178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.60915541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3781519
X-RAY DIFFRACTIONr_chiral_restr0.0590.2423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02811
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 113 -
Rwork0.247 2469 -
all-2582 -
obs--96.85 %
Refinement TLS params.Method: refined / Origin x: -8.3511 Å / Origin y: 21.7802 Å / Origin z: 15.157 Å
111213212223313233
T0.051 Å2-0.0112 Å20.0432 Å2-0.0111 Å2-0.0034 Å2--0.0417 Å2
L0.1373 °2-0.0161 °2-0.1556 °2-0.4062 °20.0102 °2--0.2889 °2
S-0.0255 Å °0.0008 Å °-0.0264 Å °0.004 Å °-0.0066 Å °0.019 Å °0.0061 Å °0.0338 Å °0.0321 Å °

+
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://pdbjlvh1.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