[English] 日本語
Yorodumi
- PDB-6uo7: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6uo7
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 (CD1) K330L mutant complexed with AR-42
ComponentsHistone deacetylase 6
KeywordsHydrolase/Hydrolase Inhibitor / Histone Deacetylase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


Aggrephagy / 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 ...Aggrephagy / 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 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
: / AR-42 / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39501316141 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: Biochemistry / Year: 2019
Title: Structural Basis of Catalysis and Inhibition of HDAC6 CD1, the Enigmatic Catalytic Domain of Histone Deacetylase 6.
Authors: Osko, J.D. / Christianson, D.W.
History
DepositionOct 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: 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 1.2Oct 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 / 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_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: Histone deacetylase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7355
Polymers40,2791
Non-polymers4564
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.000, 60.670, 121.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein Histone deacetylase 6


Mass: 40278.570 Da / Num. of mol.: 1 / Mutation: K330L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli (E. coli) / References: UniProt: F8W4B7
#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-QCP / AR-42 / N-hydroxy-4-{[(2S)-3-methyl-2-phenylbutanoyl]amino}benzamide


Mass: 312.363 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H20N2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.25 % / Description: Perfect Diamond Shape
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml HDAC6 CD1 2 mM Inhibitor 0.2 M magnesium formate dihydrate 20% PEG 3350 1:1 ratio protein to precipitant

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.39501316141→42.9865271785 Å / Num. obs: 81863 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 11.6388094639 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.032 / Net I/σ(I): 15.2
Reflection shellResolution: 1.4→1.44 Å / Rmerge(I) obs: 0.222 / Mean I/σ(I) obs: 6.8 / Num. unique obs: 8131 / CC1/2: 0.977 / Rpim(I) all: 0.094

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PHENIX1.11.1_2575refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EEF

5eef


Resolution: 1.39501316141→42.9865271785 Å / SU ML: 0.114010057186 / Cross valid method: FREE R-VALUE / σ(F): 1.4103068614 / Phase error: 17.8017587333
RfactorNum. reflection% reflection
Rfree0.184402564344 4087 4.99248744854 %
Rwork0.166169430521 --
obs0.167093471164 81863 99.941399812 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.2471834664 Å2
Refinement stepCycle: LAST / Resolution: 1.39501316141→42.9865271785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2752 0 26 384 3162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005467407221572952
X-RAY DIFFRACTIONf_angle_d0.8365152193794038
X-RAY DIFFRACTIONf_chiral_restr0.0770374993891445
X-RAY DIFFRACTIONf_plane_restr0.00589214792689531
X-RAY DIFFRACTIONf_dihedral_angle_d21.25214534061072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39501316141-1.41140.2278794953371610.1984987564222693X-RAY DIFFRACTION99.8949947497
1.4114-1.42860.2470621003141250.1945058384512603X-RAY DIFFRACTION99.9633565409
1.4286-1.44670.2335949068651340.1909915155892681X-RAY DIFFRACTION99.9644886364
1.4467-1.46580.2198939280551450.1948888833372624X-RAY DIFFRACTION99.8557518933
1.4658-1.48580.2147759980731350.1935554148182679X-RAY DIFFRACTION99.9644760213
1.4858-1.50710.2142552848781310.1859370379452618X-RAY DIFFRACTION99.9636363636
1.5071-1.52960.2128374212981430.1858173979292673X-RAY DIFFRACTION99.9290276792
1.5296-1.55350.215894072421510.1797924385572619X-RAY DIFFRACTION99.9278499278
1.5535-1.57890.2090304697351540.1733120899912641X-RAY DIFFRACTION99.9284948159
1.5789-1.60620.1956568174291480.1685355517642644X-RAY DIFFRACTION99.7855611151
1.6062-1.63540.1892363788111190.169759471082674X-RAY DIFFRACTION99.6788008565
1.6354-1.66680.1680891072751440.1663123104562672X-RAY DIFFRACTION99.9290276792
1.6668-1.70090.1826519534041310.1671955683362654X-RAY DIFFRACTION100
1.7009-1.73780.1807260451291320.1693667260442672X-RAY DIFFRACTION100
1.7378-1.77830.1618386234511350.1659039808962672X-RAY DIFFRACTION100
1.7783-1.82270.1962986834411350.1680161773592679X-RAY DIFFRACTION100
1.8227-1.8720.176388860831410.1663833299132643X-RAY DIFFRACTION100
1.872-1.92710.1746878505211350.1667432360692670X-RAY DIFFRACTION100
1.9271-1.98930.1954578996431430.1744587303882676X-RAY DIFFRACTION100
1.9893-2.06040.1872797089411180.1703365697452713X-RAY DIFFRACTION100
2.0604-2.14290.1781412954771390.1660942374952664X-RAY DIFFRACTION99.9286987522
2.1429-2.24040.2019805983161480.1659086364812691X-RAY DIFFRACTION100
2.2404-2.35850.1814979570521490.1695906294592687X-RAY DIFFRACTION100
2.3585-2.50630.1917195546691590.1674474839842693X-RAY DIFFRACTION99.9649491763
2.5063-2.69980.1877351678241470.170747380592686X-RAY DIFFRACTION100
2.6998-2.97140.1976366247791450.1674206770412738X-RAY DIFFRACTION100
2.9714-3.40120.1743986398141280.1686536870872767X-RAY DIFFRACTION100
3.4012-4.28460.1655022195631590.1459468251512747X-RAY DIFFRACTION99.8968717772
4.2846-42.98652717850.1572719300941530.1486763024662903X-RAY DIFFRACTION99.7714658831

+
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