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- PDB-8wzl: Arabidopsis thaliana Histone deacetylase 7 (HDA7) -

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Basic information

Entry
Database: PDB / ID: 8wzl
TitleArabidopsis thaliana Histone deacetylase 7 (HDA7)
ComponentsHistone deacetylase 7
KeywordsGENE REGULATION / Histone Deacetylase
Function / homology
Function and homology information


embryo sac development / seed germination / embryo development ending in seed dormancy / histone deacetylase / histone deacetylase activity / zinc ion binding / nucleus
Similarity search - Function
Histone deacetylase / : / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
Histone deacetylase 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSaharan, K. / Vasudevan, D.
Funding support India, 2items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/INF/22/SP22660/2017 India
Department of Biotechnology (DBT, India)BT/INF/22/SP33046/2019 India
CitationJournal: Curr Res Struct Biol / Year: 2024
Title: Structure-function analyses reveal Arabidopsis thaliana HDA7 to be an inactive histone deacetylase.
Authors: Saharan, K. / Baral, S. / Shaikh, N.H. / Vasudevan, D.
History
DepositionNov 2, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8764
Polymers43,5881
Non-polymers2883
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-10 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.308, 74.475, 47.590
Angle α, β, γ (deg.)90.00, 112.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Histone deacetylase 7


Mass: 43588.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: HDA7, At5g35600, K2K18.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9FH09, histone deacetylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.83 Å3/Da / Density % sol: 32.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→43.9 Å / Num. obs: 47979 / % possible obs: 98.1 % / Redundancy: 7.2 % / CC1/2: 0.93 / Net I/σ(I): 9.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2387 / CC1/2: 0.703 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→43.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.368 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19929 2458 5.1 %RANDOM
Rwork0.15715 ---
obs0.15922 45496 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.675 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20.46 Å2
2---1.34 Å2-0 Å2
3----0.54 Å2
Refinement stepCycle: 1 / Resolution: 1.5→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 15 184 3160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123069
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162790
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.6634179
X-RAY DIFFRACTIONr_angle_other_deg0.551.5786415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2965379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.691518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37710475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0880.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023642
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02724
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_it0.9191.4311507
X-RAY DIFFRACTIONr_mcbond_other0.9191.4311507
X-RAY DIFFRACTIONr_mcangle_it1.3372.5811883
X-RAY DIFFRACTIONr_mcangle_other1.3372.5821884
X-RAY DIFFRACTIONr_scbond_it1.0151.6661562
X-RAY DIFFRACTIONr_scbond_other1.0091.6511551
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4082.9492277
X-RAY DIFFRACTIONr_long_range_B_refined2.12416.463458
X-RAY DIFFRACTIONr_long_range_B_other2.05415.473426
X-RAY DIFFRACTIONr_rigid_bond_restr3.16435859
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 184 -
Rwork0.196 3302 -
obs--96.75 %

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