[English] 日本語
Yorodumi
- PDB-9gky: Crystal Structure of Histone deacetylase (HdaH) from Vibrio chole... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gky
TitleCrystal Structure of Histone deacetylase (HdaH) from Vibrio cholerae in complex with decanoic acid
ComponentsHistone deacetylase
KeywordsHYDROLASE / Deacetylase / Deacylase
Function / homology
Function and homology information


histone deacetylase activity / epigenetic regulation of gene expression / metal ion binding
Similarity search - Function
Histone deacetylase 11 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
DECANOIC ACID / IMIDAZOLE / : / Histone deacetylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsGraf, L.G. / Schulze, S. / Palm, G.J. / Lammers, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984/6-1 Germany
German Research Foundation (DFG)LA2984/8-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Distribution and diversity of classical deacylases in bacteria.
Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. ...Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. / Albrecht, D. / Zuhlke, D. / Sievers, S. / Strugnell, R.A. / Olsen, C.A. / Hofmann, K. / Lammers, M.
History
DepositionAug 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Histone deacetylase
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,80122
Polymers70,5822
Non-polymers1,21920
Water14,250791
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,88511
Polymers35,2911
Non-polymers59410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,91511
Polymers35,2911
Non-polymers62410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.11, 51.15, 108.82
Angle α, β, γ (deg.)90, 102.22, 90
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase


Mass: 35291.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion protein / Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: VN-2825 / Gene: BC353_06500 / Plasmid: pET45-b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A395TF31

-
Non-polymers , 6 types, 811 molecules

#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M Na/K tartrate, 0.1 M imidazole pH 8 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 194694 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/σ(I): 8.16
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 3.25 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 29780 / CC1/2: 0.301 / Rrim(I) all: 1.997 / Rsym value: 1.672 / % possible all: 90

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSFeb 5, 2021 BUILT=20210205data reduction
XDSFeb 5, 2021 BUILT=20210205data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→46.139 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.9 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1788 9727 4.996 %
Rwork0.1575 184963 -
all0.159 --
obs-194690 94.706 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.184 Å2-0 Å2-0.325 Å2
2--0.252 Å20 Å2
3---0.067 Å2
Refinement stepCycle: LAST / Resolution: 1.13→46.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 62 791 5691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0125362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165069
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.8187337
X-RAY DIFFRACTIONr_angle_other_deg0.6891.74911650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.367539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15310877
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.29410258
X-RAY DIFFRACTIONr_chiral_restr0.1060.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021282
X-RAY DIFFRACTIONr_nbd_refined0.2770.21281
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24554
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22594
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2530
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.25
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.250.214
X-RAY DIFFRACTIONr_nbd_other0.1530.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4660.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2190.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.190.21
X-RAY DIFFRACTIONr_mcbond_it1.2761.012613
X-RAY DIFFRACTIONr_mcbond_other1.2661.0092613
X-RAY DIFFRACTIONr_mcangle_it1.9261.8133306
X-RAY DIFFRACTIONr_mcangle_other1.9271.8143307
X-RAY DIFFRACTIONr_scbond_it2.2261.2572749
X-RAY DIFFRACTIONr_scbond_other2.2261.2572750
X-RAY DIFFRACTIONr_scangle_it3.3052.1984005
X-RAY DIFFRACTIONr_scangle_other3.3052.1984006
X-RAY DIFFRACTIONr_lrange_it5.97345.1076557
X-RAY DIFFRACTIONr_lrange_other5.63125.1386271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.1580.3646650.35712736X-RAY DIFFRACTION88.5958
1.158-1.190.3196640.32912791X-RAY DIFFRACTION90.8385
1.19-1.2250.3256650.30612579X-RAY DIFFRACTION92.4473
1.225-1.2620.2916460.28712244X-RAY DIFFRACTION93.0283
1.262-1.3040.2936230.26712073X-RAY DIFFRACTION93.649
1.304-1.3490.2666260.24811672X-RAY DIFFRACTION94.1366
1.349-1.40.2346110.22811337X-RAY DIFFRACTION95.082
1.4-1.4570.2255690.20811086X-RAY DIFFRACTION95.3998
1.457-1.5220.2165670.18610600X-RAY DIFFRACTION95.8376
1.522-1.5960.1765180.14710229X-RAY DIFFRACTION96.0669
1.596-1.6830.1654710.1399759X-RAY DIFFRACTION96.473
1.683-1.7850.1625120.1299202X-RAY DIFFRACTION96.9461
1.785-1.9080.1474060.1258775X-RAY DIFFRACTION96.8562
1.908-2.060.154410.1278113X-RAY DIFFRACTION97.2377
2.06-2.2560.1484000.127546X-RAY DIFFRACTION97.7608
2.256-2.5220.1383490.1146816X-RAY DIFFRACTION97.6823
2.522-2.9110.1493600.1245996X-RAY DIFFRACTION97.5595
2.911-3.5610.1642860.1295091X-RAY DIFFRACTION96.8829
3.561-5.0210.152330.1184047X-RAY DIFFRACTION99.1429
5.021-46.1390.1491150.1732272X-RAY DIFFRACTION96.9143
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)
10.4529-0.03360.03550.5692-0.15540.5673-0.0103-0.0156-0.0288-0.010.0090.02130.0214-0.01160.00130.02310.0004-0.01750.0230.0020.01775.0652-14.542840.2683
20.4618-0.15490.10270.6275-0.27960.6013-0.0282-0.00730.03980.0522-0.0109-0.0987-0.05590.01520.03910.02090.0028-0.02690.03010.00160.0419-16.00953.614811.5914
Refinement TLS groupSelection: ALL

+
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