[English] 日本語
Yorodumi
- PDB-7u8z: Crystal structure of Danio rerio histone deacetylase 6 catalytic ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u8z
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 (CD2) complexed with fluorinated peptoid inhibitor
ComponentsHdac6 protein
KeywordsHYDROLASE/INHIBITOR / Hydrolase / histone deacetylase / inhibitor / metallohydrolase / 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
ACETATE ION / : / Chem-M0I / MALONATE ION / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWatson, P.R. / Cragin, A.D. / 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: J.Med.Chem. / Year: 2022
Title: Development of Fluorinated Peptoid-Based Histone Deacetylase (HDAC) Inhibitors for Therapy-Resistant Acute Leukemia.
Authors: Ressing, N. / Schliehe-Diecks, J. / Watson, P.R. / Sonnichsen, M. / Cragin, A.D. / Scholer, A. / Yang, J. / Schaker-Hubner, L. / Borkhardt, A. / Christianson, D.W. / Bhatia, S. / Hansen, F.K.
History
DepositionMar 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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 25, 2023Group: 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: Hdac6 protein
B: Hdac6 protein
C: Hdac6 protein
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,25629
Polymers161,1424
Non-polymers3,11425
Water18,8621047
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9676
Polymers40,2851
Non-polymers6815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0948
Polymers40,2851
Non-polymers8087
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0006
Polymers40,2851
Non-polymers7145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1969
Polymers40,2851
Non-polymers9108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.340, 95.130, 98.139
Angle α, β, γ (deg.)90.000, 98.730, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Hdac6 protein / Histone Deacetylase 6


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

-
Non-polymers , 8 types, 1072 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-M0I / 4-({N-[2-(benzylamino)-2-oxoethyl]-4-(dimethylamino)benzamido}methyl)-3-fluoro-N-hydroxybenzamide


Mass: 478.515 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H27FN4O4
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: K
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1047 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 10 mg/mL HDAC6 protein, 2% v/v Tacsimate pH 8.0, 0.1 M Tris pH 8.5, and 16% w/v PEG 3,350

-
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: Nov 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.85→56.48 Å / Num. obs: 205228 / % possible obs: 98.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 11.65 Å2 / CC1/2: 0.98 / Net I/σ(I): 5.4
Reflection shellResolution: 1.85→1.916 Å / Num. unique obs: 19929 / CC1/2: 0.72

-
Processing

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

5eem


Resolution: 1.85→56.48 Å / SU ML: 0.2141 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.8091 / Stereochemistry target values: GeoStd + Monomer Library
Details: Calculation of the Patterson map and self rotation function indicated a peak at 27.6% of the origin. Weak reflections due to this pseudo-translation were removed.
RfactorNum. reflection% reflection
Rfree0.2154 5910 4.98 %
Rwork0.172 112856 -
obs0.1742 118766 97.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.66 Å2
Refinement stepCycle: LAST / Resolution: 1.85→56.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11092 0 158 1049 12299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006811680
X-RAY DIFFRACTIONf_angle_d0.923915877
X-RAY DIFFRACTIONf_chiral_restr0.15981710
X-RAY DIFFRACTIONf_plane_restr0.00552084
X-RAY DIFFRACTIONf_dihedral_angle_d10.19219381
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.28232040.21673762X-RAY DIFFRACTION97.76
1.87-1.890.25931910.21633694X-RAY DIFFRACTION97.64
1.89-1.920.29061800.21843749X-RAY DIFFRACTION97.76
1.92-1.940.28071780.21073728X-RAY DIFFRACTION97.43
1.94-1.970.25281870.20453778X-RAY DIFFRACTION97.93
1.97-1.990.25791780.19983735X-RAY DIFFRACTION97.8
1.99-2.020.2722070.20133753X-RAY DIFFRACTION97.54
2.02-2.050.28122150.19593699X-RAY DIFFRACTION97.44
2.05-2.080.25412070.18613724X-RAY DIFFRACTION97.28
2.08-2.120.21891940.18523702X-RAY DIFFRACTION96.77
2.12-2.150.23891850.17973713X-RAY DIFFRACTION97.21
2.15-2.190.26182100.19193743X-RAY DIFFRACTION97.94
2.19-2.240.2261900.18343788X-RAY DIFFRACTION97.91
2.24-2.280.24322030.1713736X-RAY DIFFRACTION97.81
2.28-2.330.22911860.16593696X-RAY DIFFRACTION96.69
2.33-2.390.21272150.16923693X-RAY DIFFRACTION96.88
2.39-2.440.22671850.16473804X-RAY DIFFRACTION98.4
2.44-2.510.22321960.16623793X-RAY DIFFRACTION98.79
2.51-2.580.19352020.16113794X-RAY DIFFRACTION98.81
2.58-2.670.20852000.16233738X-RAY DIFFRACTION98.43
2.67-2.760.22132000.17053781X-RAY DIFFRACTION98.59
2.76-2.870.23721970.16223832X-RAY DIFFRACTION98.87
2.87-30.19082090.16633774X-RAY DIFFRACTION98.71
3-3.160.20721810.17863819X-RAY DIFFRACTION98.26
3.16-3.360.21311960.17763763X-RAY DIFFRACTION98.36
3.36-3.620.18571870.1613823X-RAY DIFFRACTION98.67
3.62-3.990.18112010.14953763X-RAY DIFFRACTION97.44
3.99-4.560.16782110.14023793X-RAY DIFFRACTION97.87
4.56-5.750.17191940.14783830X-RAY DIFFRACTION98.7
5.75-56.480.16592210.1633856X-RAY DIFFRACTION97.91

+
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