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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eef
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 1 in complex with trichostatin A
ComponentsHDAC6
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
AMMONIUM ION / TRICHOSTATIN A / Protein deacetylase HDAC6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.151 Å
AuthorsHai, Y. / 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.Chem.Biol. / Year: 2016
Title: Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Authors: Hai, Y. / Christianson, D.W.
History
DepositionOct 22, 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 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / 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_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
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,61713
Polymers80,5892
Non-polymers1,02811
Water2,954164
1
A: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8577
Polymers40,2951
Non-polymers5626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HDAC6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7616
Polymers40,2951
Non-polymers4665
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.876, 123.717, 55.186
Angle α, β, γ (deg.)90.00, 113.85, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein HDAC6


Mass: 40294.594 Da / Num. of mol.: 2 / Fragment: catalytic domain 1 (UNP residues 60-419)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: hdac6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: F8W4B7

-
Non-polymers , 6 types, 175 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: 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.: 2 / Source method: obtained synthetically / Formula: C17H22N2O3
#4: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.96 % / Description: plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M ammonium sulfate, 0.1 M MES, pH 6.5, 25% PEG5000 MME

-
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: 2.15→45.04 Å / Num. obs: 34861 / % possible obs: 99 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 10.6
Reflection shellResolution: 2.15→2.6 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2 / % possible all: 95.9

-
Processing

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

5eek


Resolution: 2.151→45.04 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2548 1752 5.04 %
Rwork0.2106 --
obs0.2128 34749 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.151→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5518 0 63 164 5745
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045750
X-RAY DIFFRACTIONf_angle_d0.7887808
X-RAY DIFFRACTIONf_dihedral_angle_d15.9162080
X-RAY DIFFRACTIONf_chiral_restr0.03858
X-RAY DIFFRACTIONf_plane_restr0.0031014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1508-2.2090.33361190.28432447X-RAY DIFFRACTION93
2.209-2.2740.32811190.28562444X-RAY DIFFRACTION96
2.274-2.34730.32091320.26792496X-RAY DIFFRACTION98
2.3473-2.43120.28971240.27182541X-RAY DIFFRACTION98
2.4312-2.52860.31681320.26432548X-RAY DIFFRACTION100
2.5286-2.64360.31151190.25392600X-RAY DIFFRACTION100
2.6436-2.7830.32421510.24592534X-RAY DIFFRACTION100
2.783-2.95730.27591460.23292566X-RAY DIFFRACTION100
2.9573-3.18560.28791370.2292538X-RAY DIFFRACTION100
3.1856-3.50610.23651500.19812578X-RAY DIFFRACTION100
3.5061-4.01310.21821430.17582563X-RAY DIFFRACTION100
4.0131-5.05510.18381180.16132593X-RAY DIFFRACTION100
5.0551-45.040.22851620.17132549X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.188-0.0572-0.08010.0443-0.01590.08480.1384-0.0890.01140.1866-0.17490.18610.20740.358400.27760.0442-0.01370.18040.00650.2606-5.5565-35.4768-0.5096
20.0241-0.01660.11660.2050.06010.18290.0278-0.149-0.14090.088-0.0466-0.01060.0101-0.034900.2149-0.01640.00780.21210.02590.2109-19.1551-31.80255.8159
30.38640.08860.13320.3269-0.03020.43220.0651-0.0049-0.05470.02420.02560.00310.0715-0.0424-00.1321-0.0004-0.01620.0728-0.00750.1136-22.0055-30.9056-4.9485
40.40840.2718-0.08230.25360.00230.5485-0.01290.1164-0.026-0.0339-0.0229-0.0037-0.03840.087700.10320.02610.00050.0842-0.00740.0777-13.2546-22.4491-17.041
50.08370.08360.00630.02320.07290.18960.0456-0.1944-0.02090.1191-0.1972-0.0992-0.22460.3009-00.2757-0.0207-0.02380.2454-0.01760.21217.520812.298-12.5135
60.0290.06970.16250.18330.17440.0609-0.0662-0.18860.04881.57620.4811-0.80330.21390.6533-0-1.1127-0.38780.35430.4220.10680.111216.14347.179-23.2107
7-0.24260.15990.45810.0950.0970.453-0.08480.0461-0.1572-0.01220.05160.0113-0.16580.168100.0964-0.02020.00730.12360.02610.10559.26846.5237-25.7138
8-0.0101-0.02350.1330.0222-0.02050.16-0.22420.0518-0.3378-0.17220.22690.0792-0.2145-0.0056-00.17080.0478-0.02430.12060.05970.0832-5.30514.0095-34.2181
90.04380.0434-0.01170.094-0.08920.27010.7415-0.6516-0.583-0.0716-0.09230.07190.7167-0.69480-0.41880.34840.29230.0102-0.1166-0.0256-8.1551-1.2813-24.1048
100.01730.03030.08810.0657-0.09460.24670.1282-0.0412-0.01660.0141-0.1313-0.0674-0.0569-0.1167-00.11210.00590.01040.19060.00870.16-4.4756-1.0215-12.656
110.0148-0.0059-0.0226-0.002-0.02160.02920.10470.0352-0.2055-0.08640.09360.11490.2521-0.418200.1855-0.0153-0.0510.29180.03970.2945-14.8494-7.7574-33.2146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 59 through 98 )
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 134 )
3X-RAY DIFFRACTION3chain 'A' and (resid 135 through 274 )
4X-RAY DIFFRACTION4chain 'A' and (resid 275 through 417 )
5X-RAY DIFFRACTION5chain 'B' and (resid 58 through 98 )
6X-RAY DIFFRACTION6chain 'B' and (resid 99 through 135 )
7X-RAY DIFFRACTION7chain 'B' and (resid 136 through 240 )
8X-RAY DIFFRACTION8chain 'B' and (resid 241 through 274 )
9X-RAY DIFFRACTION9chain 'B' and (resid 275 through 336 )
10X-RAY DIFFRACTION10chain 'B' and (resid 337 through 394 )
11X-RAY DIFFRACTION11chain 'B' and (resid 395 through 417 )

+
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