[English] 日本語
Yorodumi
- PDB-5eek: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eek
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with trichostatin A
ComponentsHdac6 protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


negative regulation of cellular component organization / positive regulation of cellular component organization / Aggrephagy / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process ...negative regulation of cellular component organization / positive regulation of cellular component organization / Aggrephagy / regulation of biological quality / deacetylase activity / tubulin deacetylase activity / mitochondrion localization / swimming behavior / definitive hemopoiesis / regulation of microtubule-based process / protein lysine deacetylase activity / histone deacetylase activity / response to stress / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / epigenetic regulation of gene expression / transferase activity / actin binding / chromatin organization / angiogenesis / perikaryon / axon / dendrite / centrosome / zinc ion binding / nucleus / cytoplasm / cytosol
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 ...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
IODIDE ION / : / AMMONIUM ION / TRICHOSTATIN A / Protein deacetylase HDAC6 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsHai, Y. / Christianson, D.W.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Authors: Hai, Y. / Christianson, D.W.
History
DepositionOct 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 7, 2016Group: Database references
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,39141
Polymers40,2851
Non-polymers4,10540
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-46 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.881, 94.429, 51.698
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2007-

IOD

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Hdac6 protein / histone deacetylase 6


Mass: 40285.484 Da / Num. of mol.: 1 / Fragment: catalytic domain 2 (UNP residues 288-646)
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, histone deacetylase

-
Non-polymers , 9 types, 416 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-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N2O3
#5: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: I
#6: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: H4N
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M ammonium iodide, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.28184 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 23, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28184 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. all: 56038 / Num. obs: 55924 / % possible obs: 100 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 23.7
Reflection shellResolution: 1.59→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.3 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5EEI

5eei


Resolution: 1.59→44.011 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1631 2843 5.08 %
Rwork0.1295 --
obs0.1313 55910 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→44.011 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 72 376 3225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092948
X-RAY DIFFRACTIONf_angle_d1.2964005
X-RAY DIFFRACTIONf_dihedral_angle_d14.4131086
X-RAY DIFFRACTIONf_chiral_restr0.056433
X-RAY DIFFRACTIONf_plane_restr0.007526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5903-1.61770.20641280.13492622X-RAY DIFFRACTION100
1.6177-1.64720.17221390.12212628X-RAY DIFFRACTION100
1.6472-1.67880.16951220.11762615X-RAY DIFFRACTION100
1.6788-1.71310.16681270.11922624X-RAY DIFFRACTION100
1.7131-1.75040.1621480.11362636X-RAY DIFFRACTION100
1.7504-1.79110.17861390.11132627X-RAY DIFFRACTION100
1.7911-1.83590.15251370.1092606X-RAY DIFFRACTION100
1.8359-1.88550.15091530.11092617X-RAY DIFFRACTION100
1.8855-1.9410.14981240.11162635X-RAY DIFFRACTION100
1.941-2.00360.14721290.10722674X-RAY DIFFRACTION100
2.0036-2.07520.15141440.11442615X-RAY DIFFRACTION100
2.0752-2.15830.16791370.12312649X-RAY DIFFRACTION100
2.1583-2.25660.15481490.12072638X-RAY DIFFRACTION100
2.2566-2.37550.15671350.11922654X-RAY DIFFRACTION100
2.3755-2.52430.17491470.13072666X-RAY DIFFRACTION100
2.5243-2.71920.1531630.13532654X-RAY DIFFRACTION100
2.7192-2.99280.16851430.14132660X-RAY DIFFRACTION100
2.9928-3.42570.17431690.14772672X-RAY DIFFRACTION100
3.4257-4.31550.16271560.13052724X-RAY DIFFRACTION100
4.3155-44.02740.16191540.15592851X-RAY DIFFRACTION100

+
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