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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dvn
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with DDK-137
ComponentsHdac6 protein
Keywordshydrolase/hydrolase inhibitor / Histone deacetylase / metallohydrolase / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...Aggrephagy / negative regulation of cellular component organization / positive regulation of cellular component organization / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / potassium ion binding / response to stress / hematopoietic progenitor cell differentiation / transferase activity / chromatin organization / actin binding / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytosol / cytoplasm
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 domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain ...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 domain / Arginase; Chain A / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Zinc finger, RING/FYVE/PHD-type / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HB7 / : / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOsko, J.D. / Christianson, D.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM49758 United States
CitationJournal: J. Med. Chem. / Year: 2018
Title: Histone Deacetylase 6-Selective Inhibitors and the Influence of Capping Groups on Hydroxamate-Zinc Denticity.
Authors: Porter, N.J. / Osko, J.D. / Diedrich, D. / Kurz, T. / Hooker, J.M. / Hansen, F.K. / Christianson, D.W.
History
DepositionJun 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _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: Hdac6 protein
B: Hdac6 protein
C: Hdac6 protein
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,86925
Polymers161,1424
Non-polymers2,72721
Water3,477193
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0147
Polymers40,2851
Non-polymers7286
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9526
Polymers40,2851
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9526
Polymers40,2851
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9526
Polymers40,2851
Non-polymers6665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.550, 95.500, 98.250
Angle α, β, γ (deg.)90.00, 98.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Hdac6 protein


Mass: 40285.484 Da / Num. of mol.: 4
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, UniProt: F8W4B7*PLUS

-
Non-polymers , 5 types, 214 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-HB7 / N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)-N-{[4-(hydroxycarbamoyl)phenyl]methyl}benzamide


Mass: 460.525 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H28N4O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.26 Å3/Da / Density % sol: 45.6 % / Description: Plate crystals
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M ammonium tartrate dibasic (7.0), 20% w/v PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.18 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18 Å / Relative weight: 1
ReflectionResolution: 2.2→95.5 Å / Num. obs: 69939 / % possible obs: 96 % / Redundancy: 5.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.102 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 5 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6728 / CC1/2: 0.721 / Rpim(I) all: 0.371 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEM

5eem


Resolution: 2.2→48.573 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.51
RfactorNum. reflection% reflection
Rfree0.2228 3459 4.95 %
Rwork0.1881 --
obs0.1899 69939 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→48.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11062 0 168 193 11423
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311564
X-RAY DIFFRACTIONf_angle_d0.59815713
X-RAY DIFFRACTIONf_dihedral_angle_d16.3636838
X-RAY DIFFRACTIONf_chiral_restr0.0431704
X-RAY DIFFRACTIONf_plane_restr0.0042058
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.23010.32441550.24622579X-RAY DIFFRACTION94
2.2301-2.2620.29751450.23982479X-RAY DIFFRACTION91
2.262-2.29580.2581310.22122609X-RAY DIFFRACTION93
2.2958-2.33160.25981320.21472704X-RAY DIFFRACTION98
2.3316-2.36990.25711550.22462676X-RAY DIFFRACTION98
2.3699-2.41070.31431300.21192681X-RAY DIFFRACTION97
2.4107-2.45460.2591480.21222721X-RAY DIFFRACTION98
2.4546-2.50180.24271390.21322656X-RAY DIFFRACTION97
2.5018-2.55280.23781360.20442695X-RAY DIFFRACTION97
2.5528-2.60830.26231560.20622626X-RAY DIFFRACTION96
2.6083-2.6690.26451370.20512670X-RAY DIFFRACTION96
2.669-2.73580.25531330.21132698X-RAY DIFFRACTION96
2.7358-2.80970.27431150.21582663X-RAY DIFFRACTION95
2.8097-2.89240.25071020.21392530X-RAY DIFFRACTION90
2.8924-2.98570.28011350.22032687X-RAY DIFFRACTION97
2.9857-3.09240.24271450.21172694X-RAY DIFFRACTION98
3.0924-3.21620.21461390.20612713X-RAY DIFFRACTION98
3.2162-3.36260.23771470.2032717X-RAY DIFFRACTION98
3.3626-3.53980.22761520.1882686X-RAY DIFFRACTION97
3.5398-3.76150.21291350.16712680X-RAY DIFFRACTION96
3.7615-4.05180.17241170.15772560X-RAY DIFFRACTION92
4.0518-4.45930.15681360.1412575X-RAY DIFFRACTION92
4.4593-5.10390.14651600.13282724X-RAY DIFFRACTION99
5.1039-6.42810.16511390.15852758X-RAY DIFFRACTION98
6.4281-48.58450.14861400.12882699X-RAY DIFFRACTION94

+
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