[English] 日本語
Yorodumi
- PDB-7vmi: Crystal structure of Arabidopsis thaliana HDT3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vmi
TitleCrystal structure of Arabidopsis thaliana HDT3
ComponentsHistone deacetylase HDT3
KeywordsCHAPERONE / HDT / HD-tuin / Nucleoplasmin / Histone chaperone / HD2C / HDT3
Function / homology
Function and homology information


response to abscisic acid / response to water deprivation / response to salt stress / response to cold / chromatin organization / hydrolase activity / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / nucleolus / metal ion binding / plasma membrane
Similarity search - Function
Nucleoplasmin-like domain / Nucleoplasmin-like domain / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Histone deacetylase HDT3
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBobde, R.C. / Kumar, A. / Vasudevan, D.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India) India
Science and Engineering Research Board (SERB) India
CitationJournal: Plant Cell / Year: 2022
Title: Plant-specific HDT family histone deacetylases are nucleoplasmins.
Authors: Bobde, R.C. / Kumar, A. / Vasudevan, D.
History
DepositionOct 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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: Histone deacetylase HDT3
B: Histone deacetylase HDT3
C: Histone deacetylase HDT3
D: Histone deacetylase HDT3
E: Histone deacetylase HDT3


Theoretical massNumber of molelcules
Total (without water)53,8915
Polymers53,8915
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-44 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.623, 77.600, 55.511
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Histone deacetylase HDT3 / HD-tuins protein 3 / Histone deacetylase 2c


Mass: 10778.290 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDT3, HD2C, At5g03740, F17C15_160, MED24.1 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9LZR5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M succinic acid pH 7.0, 0.1 M bicine, 30% V/V PEG MME 550

-
Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.75→45.13 Å / Num. obs: 46503 / % possible obs: 99.5 % / Redundancy: 3.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.051 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2562 / CC1/2: 0.869 / Rrim(I) all: 0.678 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VMF

7vmf


Resolution: 1.8→35.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.961 / SU B: 9.812 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2164 5.1 %RANDOM
Rwork0.19 ---
obs0.191 40545 99.4 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.76 Å2
Baniso -1Baniso -2Baniso -3
1--4.63 Å20 Å2-0.41 Å2
2--7.64 Å20 Å2
3----2.98 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 0 116 3917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0183891
X-RAY DIFFRACTIONr_bond_other_d0.0010.023722
X-RAY DIFFRACTIONr_angle_refined_deg1.7591.8765276
X-RAY DIFFRACTIONr_angle_other_deg1.1032.8038595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0915475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82624.167180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72915676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5231510
X-RAY DIFFRACTIONr_chiral_restr0.1130.2600
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6720.8841915
X-RAY DIFFRACTIONr_mcbond_other1.6650.8831914
X-RAY DIFFRACTIONr_mcangle_it2.7831.3122385
X-RAY DIFFRACTIONr_mcangle_other2.7821.3142386
X-RAY DIFFRACTIONr_scbond_it2.0541.0651976
X-RAY DIFFRACTIONr_scbond_other2.0541.0671977
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.1681.522892
X-RAY DIFFRACTIONr_long_range_B_refined6.09510.9124045
X-RAY DIFFRACTIONr_long_range_B_other6.09910.7174018
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 178 -
Rwork0.292 2986 -
obs--99.84 %
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)
12.7524-0.3940.45932.01010.21192.8729-0.14140.80990.2131-0.22510.1559-0.2084-0.26710.4718-0.01440.3505-0.12120.03510.40780.01890.339529.4762.875.557
24.04340.41810.11192.06010.31031.6866-0.07450.01410.31580.1049-0.03330.1234-0.1327-0.13780.10790.34490.0169-0.01130.0118-0.01560.33511.6055.23221.71
33.55490.83760.71222.50220.22652.51350.05-0.5221-0.29470.1554-0.0577-0.08280.10580.00880.00770.3125-0.00210.0160.08420.03520.313512.774-8.70330.462
43.72320.03210.41891.93830.58632.5658-0.12490.68090.6256-0.16610.02890.1077-0.38590.00680.0960.4244-0.0735-0.03390.21150.17630.426411.93512.4616.358
54.55690.0848-0.72391.72270.03841.9488-0.05620.1146-0.48880.08260.1123-0.23090.13120.4126-0.05610.31580.011-0.00710.125-0.04220.36630.095-9.90820.633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 96
2X-RAY DIFFRACTION2B1 - 96
3X-RAY DIFFRACTION3C1 - 96
4X-RAY DIFFRACTION4D1 - 96
5X-RAY DIFFRACTION5E1 - 96

+
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