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- PDB-7vrr: Crystal structure of Arabidopsis thaliana HDT1 -

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Basic information

Entry
Database: PDB / ID: 7vrr
TitleCrystal structure of Arabidopsis thaliana HDT1
ComponentsHistone deacetylase HDT1
KeywordsCHAPERONE / HDAC / HD-tuin / HDT / Histone deactylase / nucleoplasmin
Function / homology
Function and homology information


polarity specification of adaxial/abaxial axis / seed dormancy process / DNA-mediated transformation / root development / histone deacetylase activity / chromatin organization / negative regulation of DNA-templated transcription / nucleolus / metal ion binding
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 HDT1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsKumar, A. / Bobde, R.C. / Vasudevan, D.
Funding support India, 1items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)CRG/2018/000695 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase HDT1
B: Histone deacetylase HDT1
C: Histone deacetylase HDT1
D: Histone deacetylase HDT1
E: Histone deacetylase HDT1


Theoretical massNumber of molelcules
Total (without water)53,3965
Polymers53,3965
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-61 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.961, 79.961, 143.625
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Histone deacetylase HDT1 / HD-tuins protein 1 / Histone deacetylase 2a


Mass: 10679.218 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDT1, HD2A, HDA3, At3g44750, T32N15.8 / Plasmid: pet22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FVE6

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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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 301 K / Method: vapor diffusion / pH: 7.5
Details: 50 mM MgCl2.6H2O, 0.1M HEPES (pH 7.5), 30% V/V PEG MME 550

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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: Jan 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.95→44.42 Å / Num. obs: 10405 / % possible obs: 100 % / Redundancy: 9.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.12 / Net I/σ(I): 20.2
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1621 / CC1/2: 0.928 / Rsym value: 0.705 / % possible all: 100

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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: 2.95→41.11 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.247 --
Rwork0.224 --
obs-9849 99.91 %
Refinement stepCycle: LAST / Resolution: 2.95→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 0 0 3554
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0183670
X-RAY DIFFRACTIONr_bond_other_d0.0010.023484
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.8794965
X-RAY DIFFRACTIONr_angle_other_deg0.952.8248079
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995443
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.12425.733150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.32715628
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02758
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 32 -
Rwork0.319 698 -
obs--100 %
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)
15.64620.48310.33646.0354-1.96445.3526-0.01810.12820.40690.041-0.159-0.3789-0.51110.00890.17710.1007-0.054-0.05810.08570.10530.185821.13775.749-5.942
23.64060.79141.91484.9892-1.65195.90380.10970.24190.0802-0.4983-0.15560.27840.3598-0.29790.04590.1552-0.0315-0.08010.12640.01260.05419.49661.005-11.594
35.25410.26420.05046.7127-0.66763.8497-0.0983-0.32790.10260.9439-0.312-0.8205-0.26320.46730.41030.2646-0.119-0.2680.12610.12170.321730.09270.39610.665
44.7534-0.92182.43468.5485-1.99055.85030.0616-0.37270.02660.7427-0.1809-0.4602-0.0687-0.0950.11920.1996-0.0899-0.12030.0750.05980.086123.99952.25415.357
54.39880.13621.33756.5539-2.20296.33990.19690.1031-0.1774-0.20880.07440.60.6245-0.3573-0.27130.2405-0.1268-0.07290.0790.02650.074111.37246.4691.549
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 96
2X-RAY DIFFRACTION2B1 - 95
3X-RAY DIFFRACTION3C1 - 95
4X-RAY DIFFRACTION4D1 - 96
5X-RAY DIFFRACTION5E1 - 95

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