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- PDB-7vmh: Crystal structure of Arabidopsis thaliana HDT4 -

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Basic information

Entry
Database: PDB / ID: 7vmh
TitleCrystal structure of Arabidopsis thaliana HDT4
ComponentsHistone deacetylase HDT4
KeywordsCHAPERONE / HDT / HD-tuin / Nucleoplasmin / Histone chaperone / HD2D / HDT4
Function / homologyseed dormancy process / Nucleoplasmin-like domain / Nucleoplasmin-like domain / chromatin organization / hydrolase activity / nucleolus / Histone deacetylase HDT4
Function and homology information
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase HDT4
B: Histone deacetylase HDT4
C: Histone deacetylase HDT4
D: Histone deacetylase HDT4
E: Histone deacetylase HDT4


Theoretical massNumber of molelcules
Total (without water)59,4325
Polymers59,4325
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8330 Å2
ΔGint-70 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.482, 73.114, 72.580
Angle α, β, γ (deg.)90.00, 96.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Histone deacetylase HDT4 / HD-tuins protein 4 / Histone deacetylase 2d


Mass: 11886.490 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDT4, HD2D, HDA13, At2g27840, F15K20.6 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9M4T3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 38.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M l-proline, 0.1 m HEPES pH 7.5, 24% W/V PEG 1500

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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: Jul 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.85→46.29 Å / Num. obs: 38947 / % possible obs: 96.9 % / Redundancy: 3.7 % / CC1/2: 0.997 / Net I/σ(I): 10.9
Reflection shellResolution: 1.85→1.89 Å / Redundancy: 3.7 % / Num. unique obs: 2203 / CC1/2: 0.819 / % possible all: 88.6

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Processing

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

7vmf


Resolution: 1.85→44.96 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.884 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22843 1969 5.1 %RANDOM
Rwork0.19293 ---
obs0.1948 37002 96.94 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.881 Å2
Baniso -1Baniso -2Baniso -3
1-2.6 Å2-0 Å20.18 Å2
2---0.98 Å2-0 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3903 0 0 110 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0184013
X-RAY DIFFRACTIONr_bond_other_d0.0010.023736
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.8615394
X-RAY DIFFRACTIONr_angle_other_deg1.0832.8118653
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.98624.541196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73215714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg30.753155
X-RAY DIFFRACTIONr_chiral_restr0.1140.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024476
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
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_it2.7762.6731931
X-RAY DIFFRACTIONr_mcbond_other2.7672.6711930
X-RAY DIFFRACTIONr_mcangle_it4.1693.9762402
X-RAY DIFFRACTIONr_mcangle_other4.1683.9782403
X-RAY DIFFRACTIONr_scbond_it3.6013.2172082
X-RAY DIFFRACTIONr_scbond_other3.63.222083
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6424.62992
X-RAY DIFFRACTIONr_long_range_B_refined7.54530.5614133
X-RAY DIFFRACTIONr_long_range_B_other7.55330.5664128
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 139 -
Rwork0.265 2499 -
obs--88.94 %

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