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- PDB-9gz5: X-ray structure of Leptospira interrogans Histone deacetylase 11 ... -

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Basic information

Entry
Database: PDB / ID: 9gz5
TitleX-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid.
ComponentsHistone deacetylase
KeywordsHYDROLASE / Histone deacetylase 11 / Leptospira interrogans / class IV HDAC / zinc binding group
Function / homology
Function and homology information


histone deacetylase activity / epigenetic regulation of gene expression
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
: / : / Histone deacetylase
Similarity search - Component
Biological speciesLeptospira interrogans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsNovakova, Z. / Barinka, C. / Motlova, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of Leptospira interrogans Histone deacetylase 11 (HDAC11) in complex with cis-5-dodecenoic acid.
Authors: Novakova, Z. / Barinka, C. / Motlova, L.
History
DepositionOct 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6848
Polymers35,0731
Non-polymers6117
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint4 kcal/mol
Surface area12820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.265, 61.744, 49.481
Angle α, β, γ (deg.)90.00, 99.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Histone deacetylase


Mass: 35072.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans (bacteria) / Gene: acuC, LA_2923 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8F254

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Non-polymers , 6 types, 156 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-A1IRB / cis-5-dodecenoic acid / (~{E})-dodec-5-enoic acid


Mass: 198.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.07 Å3/Da / Density % sol: 40.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 1 protein:2 precipitant 100 mM HEPES pH 7.4, 200 mM MgCl2, 23% PEG3350

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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 S 6M / Detector: PIXEL / Date: May 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.55→48.75 Å / Num. obs: 40698 / % possible obs: 98.7 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.048 / Net I/σ(I): 13
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.681 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1844 / CC1/2: 0.451 / Rpim(I) all: 0.621 / % possible all: 91.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimlessdata scaling
XDSdata reduction
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.665 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20071 2020 5 %RANDOM
Rwork0.17295 ---
obs0.17438 38658 98.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.427 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-0.58 Å2
2---0.74 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.55→48.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 36 149 2635
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9713540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2524.462130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92815455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.3421511
X-RAY DIFFRACTIONr_chiral_restr0.1090.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212009
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.2691.9021244
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8242.8481569
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3042.1971375
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.82916.8024211
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: 1.555→1.595 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 134 -
Rwork0.284 2742 -
obs--94.14 %

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