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- PDB-7vmf: Crystal structure of Arabidopsis thaliana HDT2 -

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Basic information

Entry
Database: PDB / ID: 7vmf
TitleCrystal structure of Arabidopsis thaliana HDT2
ComponentsHistone deacetylase HDT2
KeywordsCHAPERONE / HDT / HD-tuin / Nucleoplasmin / Histone chaperone / HD2B / HDT2
Function / homology
Function and homology information


polarity specification of adaxial/abaxial axis / seed dormancy process / DNA-mediated transformation / root development / plant-type cell wall / plant-type vacuole / plastid / histone deacetylase activity / negative regulation of DNA-templated transcription / nucleolus ...polarity specification of adaxial/abaxial axis / seed dormancy process / DNA-mediated transformation / root development / plant-type cell wall / plant-type vacuole / plastid / histone deacetylase activity / negative regulation of DNA-templated transcription / nucleolus / mitochondrion / nucleus
Similarity search - Function
Nucleoplasmin-like domain / Nucleoplasmin-like domain
Similarity search - Domain/homology
Histone deacetylase HDT2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsKumar, A. / Bobde, R.C. / 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 HDT2
B: Histone deacetylase HDT2
C: Histone deacetylase HDT2
D: Histone deacetylase HDT2
E: Histone deacetylase HDT2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8526
Polymers51,8295
Non-polymers231
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8100 Å2
ΔGint-55 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.106, 96.221, 196.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Histone deacetylase HDT2 / HD-tuins protein 2 / Histone deacetylase 2b


Mass: 10365.731 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDT2, HD2, HD2B, HDA4, At5g22650, MDJ22.7 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q56WH4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2M ammonium phosphate dibasic pH-8.0, 20%W/V PEG 3350

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Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07227 Å / Relative weight: 1
ReflectionResolution: 1.32→49.07 Å / Num. obs: 111734 / % possible obs: 95 % / Redundancy: 3.6 % / CC1/2: 0.999 / Net I/σ(I): 13.9
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4443 / CC1/2: 0.853 / % possible all: 77.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J2Z

6j2z


Resolution: 1.32→46.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.786 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18915 5549 5 %RANDOM
Rwork0.16015 ---
obs0.1616 106115 94.59 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.148 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0 Å20 Å2
2--0.5 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.32→46.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 1 330 3944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0183695
X-RAY DIFFRACTIONr_bond_other_d0.0010.023501
X-RAY DIFFRACTIONr_angle_refined_deg1.711.8735011
X-RAY DIFFRACTIONr_angle_other_deg1.0532.8538137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.11526.071140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83615631
X-RAY DIFFRACTIONr_chiral_restr0.1180.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024112
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02740
X-RAY DIFFRACTIONr_mcbond_it1.9691.9381901
X-RAY DIFFRACTIONr_mcbond_other1.9681.9371900
X-RAY DIFFRACTIONr_mcangle_it2.5362.9172368
X-RAY DIFFRACTIONr_mcangle_other2.5362.9192369
X-RAY DIFFRACTIONr_scbond_it2.792.341794
X-RAY DIFFRACTIONr_scbond_other2.7892.3411795
X-RAY DIFFRACTIONr_scangle_other3.373.3382643
X-RAY DIFFRACTIONr_long_range_B_refined3.65124.3593792
X-RAY DIFFRACTIONr_long_range_B_other3.62824.0863715
X-RAY DIFFRACTIONr_rigid_bond_restr3.22837196
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 341 -
Rwork0.213 6472 -
obs--78.84 %

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