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- PDB-9rje: X-ray structure of Chlamydomonas reinhardtii Histone Deacetylase ... -

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Basic information

Entry
Database: PDB / ID: 9rje
TitleX-ray structure of Chlamydomonas reinhardtii Histone Deacetylase 11 (HDAC11) in complex with hexanoic acid
ComponentsHistone deacetylase domain-containing protein
KeywordsUNKNOWN FUNCTION / Histone deacetylase 11 / Chlamydomonas reinhardtii / class IV HDAC / zinc binding group / fatty acid
Function / homology
Function and homology information


histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity
Similarity search - Function
Histone deacetylase 11 / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
HEXANOIC ACID / : / NITRATE ION / Histone deacetylase domain-containing protein
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsNovakova, Z. / Schenkmayerova, A. / Motlova, L. / Barinka, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of Chlamydomonas reinhardtii Histone Deacetylase 11 (HDAC11) in complex with hexanoic acid
Authors: Novakova, Z. / Schenkmayerova, A. / Motlova, L. / Barinka, C.
History
DepositionJun 12, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone deacetylase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,17312
Polymers34,5181
Non-polymers65511
Water9,944552
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.660, 90.040, 102.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase domain-containing protein


Mass: 34518.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HD11 from Chlamydomonas reinhardtii AA 71-385. GGGT 1-4 belongs to linker
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_14g632300v5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2K3CYT6

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Non-polymers , 9 types, 563 molecules

#2: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: Precipitant: 0.1 M Bis-Tris, 0.2 M sodium nitrate, 15% PEG 3350, 15% glycerol, pH 6.6 SEC Buffer:25 mM Tris-HCl, 140 mM NaCl, 100 mM KCl, 3% glycerol, pH 8 cryoprotection: 20% glycerol in precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 25, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.04→50 Å / Num. obs: 174843 / % possible obs: 97.9 % / Redundancy: 12.48 % / Biso Wilson estimate: 7.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.72
Reflection shellResolution: 1.04→1.1 Å / Rmerge(I) obs: 1.135 / Mean I/σ(I) obs: 2.13 / Num. unique obs: 26066 / CC1/2: 0.741 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.06→32.07 Å / SU ML: 0.0988 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1649 2099 1.26 %Random selection
Rwork0.1422 164518 --
obs0.1425 166617 98.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.68 Å2
Refinement stepCycle: LAST / Resolution: 1.06→32.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2434 0 35 552 3021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00392749
X-RAY DIFFRACTIONf_angle_d0.78463761
X-RAY DIFFRACTIONf_chiral_restr0.0745409
X-RAY DIFFRACTIONf_plane_restr0.0092515
X-RAY DIFFRACTIONf_dihedral_angle_d11.83511038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.06-1.080.3561310.27910261X-RAY DIFFRACTION93.29
1.08-1.110.21831370.218810721X-RAY DIFFRACTION97.49
1.11-1.140.23041380.190710818X-RAY DIFFRACTION98.19
1.14-1.180.16281380.168910848X-RAY DIFFRACTION98.4
1.18-1.210.18551390.159510887X-RAY DIFFRACTION98.73
1.21-1.260.16991400.155310953X-RAY DIFFRACTION98.9
1.26-1.310.1491400.140610940X-RAY DIFFRACTION99.12
1.31-1.370.15331400.13810985X-RAY DIFFRACTION99.35
1.37-1.440.16651410.129511052X-RAY DIFFRACTION99.58
1.44-1.530.1361410.11811036X-RAY DIFFRACTION99.63
1.53-1.650.13431410.113511068X-RAY DIFFRACTION99.88
1.65-1.810.1631420.121911137X-RAY DIFFRACTION99.99
1.81-2.070.14071420.131411111X-RAY DIFFRACTION99.4
2.07-2.610.15951430.137411189X-RAY DIFFRACTION99.63
2.61-32.070.16341460.135411512X-RAY DIFFRACTION99.82

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