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

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6css
TitleCrystal structure of Danio rerio histone deacetylase 6 catalytic domain 2 in complex with cyclopentenylhydroxamate
ComponentsHdac6 protein
KeywordsHYDROLASE / Zinc hydrolase / tubulin deacetylase
Function / homology
Function and homology information


: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding ...: / Aggrephagy / : / tubulin deacetylase activity / swimming behavior / definitive hemopoiesis / protein lysine deacetylase activity / histone deacetylase activity / regulation of tubulin deacetylation / potassium ion binding / histone deacetylase complex / hematopoietic progenitor cell differentiation / angiogenesis / negative regulation of transcription by RNA polymerase II / 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 / 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
N-hydroxycyclopent-1-ene-1-carboxamide / : / Hdac6 protein / Histone deacetylase 6
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsPorter, N.J. / 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: Biochemistry / Year: 2018
Title: Entropy as a Driver of Selectivity for Inhibitor Binding to Histone Deacetylase 6.
Authors: Porter, N.J. / Wagner, F.F. / Christianson, D.W.
History
DepositionMar 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,67119
Polymers80,5712
Non-polymers1,10017
Water11,782654
1
A: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,92911
Polymers40,2851
Non-polymers64310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hdac6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7428
Polymers40,2851
Non-polymers4577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.791, 92.021, 96.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Hdac6 protein /


Mass: 40285.484 Da / Num. of mol.: 2
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, 671 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-FBJ / N-hydroxycyclopent-1-ene-1-carboxamide / cyclopentenylhydroxamate


Mass: 127.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 654 / 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: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium tartrate 20% PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.7→96.64 Å / Num. obs: 74006 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.091 / Rrim(I) all: 0.242 / Net I/σ(I): 8.6 / Num. measured all: 507763 / Scaling rejects: 256
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.736.31.5582452138650.6050.671.73.4100
9-96.645.80.06834695950.9940.0290.07513.799.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→48.32 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 3819 5.17 %
Rwork0.1695 70041 -
obs0.1707 73860 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.59 Å2 / Biso mean: 10.9494 Å2 / Biso min: 0.85 Å2
Refinement stepCycle: final / Resolution: 1.7→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 60 654 6287
Biso mean--18.98 22.53 -
Num. residues----715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035892
X-RAY DIFFRACTIONf_angle_d0.6977996
X-RAY DIFFRACTIONf_chiral_restr0.049865
X-RAY DIFFRACTIONf_plane_restr0.0051050
X-RAY DIFFRACTIONf_dihedral_angle_d17.6933524
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72150.26081310.231325442675100
1.7215-1.74420.25161460.215725762722100
1.7442-1.76810.23491570.195825162673100
1.7681-1.79330.2311240.185125832707100
1.7933-1.82010.22411250.188225842709100
1.8201-1.84860.23171100.188425812691100
1.8486-1.87890.2151400.183125852725100
1.8789-1.91130.19751380.18325982736100
1.9113-1.9460.20811310.179725412672100
1.946-1.98350.22421420.181125762718100
1.9835-2.02390.21151710.176525552726100
2.0239-2.06790.2151530.171825582711100
2.0679-2.11610.19911540.162925632717100
2.1161-2.1690.21771470.168525602707100
2.169-2.22760.17481550.167525812736100
2.2276-2.29320.19191640.166625382702100
2.2932-2.36720.18271480.168225872735100
2.3672-2.45180.17751010.159926282729100
2.4518-2.54990.17541210.166426212742100
2.5499-2.6660.20721350.170126112746100
2.666-2.80650.17491350.168225862721100
2.8065-2.98230.17411380.171626462784100
2.9823-3.21260.19231510.172325942745100
3.2126-3.53580.1761460.159926232769100
3.5358-4.04720.15011400.141126562796100
4.0472-5.09810.16981720.143426602832100
5.0981-48.33950.18371440.16772790293499

+
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