[English] 日本語
Yorodumi
- PDB-6wsj: Crystal Structure of Danio rerio histone deacetylase 6 catalytic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wsj
TitleCrystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.3.1
Components
  • Hdac6 protein
  • cyclopeptide des4.3.1
Keywordshydrolase/hydrolase inhibitor / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / angiogenesis / zinc ion binding
Similarity search - Function
Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger / Zinc finger, UBP-type / Zn-finger in ubiquitin-hydrolases and other protein / Zinc finger UBP-type profile. / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
des4.3.1 / : / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWatson, P.R. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49758 United States
CitationJournal: Nat Commun / Year: 2021
Title: Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.
Authors: Hosseinzadeh, P. / Watson, P.R. / Craven, T.W. / Li, X. / Rettie, S. / Pardo-Avila, F. / Bera, A.K. / Mulligan, V.K. / Lu, P. / Ford, A.S. / Weitzner, B.D. / Stewart, L.J. / Moyer, A.P. / Di ...Authors: Hosseinzadeh, P. / Watson, P.R. / Craven, T.W. / Li, X. / Rettie, S. / Pardo-Avila, F. / Bera, A.K. / Mulligan, V.K. / Lu, P. / Ford, A.S. / Weitzner, B.D. / Stewart, L.J. / Moyer, A.P. / Di Piazza, M. / Whalen, J.G. / Greisen, P.J. / Christianson, D.W. / Baker, D.
History
DepositionMay 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hdac6 protein
I: cyclopeptide des4.3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5507
Polymers41,2832
Non-polymers2685
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-36 kcal/mol
Surface area13110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.500, 84.000, 94.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

-
Components

-
Protein / Protein/peptide , 2 types, 2 molecules AI

#1: Protein Hdac6 protein / Histone Deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: A7YT55
#2: Protein/peptide cyclopeptide des4.3.1


Type: Cyclic peptide / Class: Enzyme inhibitor / Mass: 997.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: des4.3.1

-
Non-polymers , 4 types, 244 molecules

#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 protein 0.2 M ammonium chloride and 20% polyethylene glycol (PEG) 3350 (w/v)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→62.76 Å / Num. obs: 45672 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.48 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.079 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 45672 / CC1/2: 0.845 / Rpim(I) all: 0.413

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 5EEM

5eem


Resolution: 1.7→62.76 Å / SU ML: 0.1623 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.3393 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1764 2204 4.83 %
Rwork0.154 43453 -
obs0.1551 45657 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.88 Å2
Refinement stepCycle: LAST / Resolution: 1.7→62.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2725 0 79 239 3043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00592897
X-RAY DIFFRACTIONf_angle_d0.9633929
X-RAY DIFFRACTIONf_chiral_restr0.0569429
X-RAY DIFFRACTIONf_plane_restr0.0057512
X-RAY DIFFRACTIONf_dihedral_angle_d8.31852917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.2481120.19512677X-RAY DIFFRACTION99.96
1.74-1.780.21251450.182693X-RAY DIFFRACTION99.96
1.78-1.820.20781220.15442677X-RAY DIFFRACTION99.96
1.82-1.870.19851210.1492685X-RAY DIFFRACTION99.96
1.87-1.930.18031250.14352700X-RAY DIFFRACTION100
1.93-1.990.16771320.14172697X-RAY DIFFRACTION100
1.99-2.060.17591360.15662706X-RAY DIFFRACTION100
2.06-2.140.1781400.14592694X-RAY DIFFRACTION100
2.14-2.240.16461310.14542691X-RAY DIFFRACTION99.93
2.24-2.360.16961600.14492656X-RAY DIFFRACTION100
2.36-2.510.14781442702X-RAY DIFFRACTION100
2.51-2.70.20311430.15672721X-RAY DIFFRACTION99.9
2.7-2.970.18091510.16132717X-RAY DIFFRACTION99.97
2.97-3.40.20041450.16662750X-RAY DIFFRACTION99.9
3.4-4.290.16171280.14882810X-RAY DIFFRACTION100
4.29-62.760.15251690.14882877X-RAY DIFFRACTION99.87

+
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