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- PDB-9gky: Crystal Structure of Histone deacetylase (HdaH) from Vibrio chole... -

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Basic information

Entry
Database: PDB / ID: 9gky
TitleCrystal Structure of Histone deacetylase (HdaH) from Vibrio cholerae in complex with decanoic acid
ComponentsHistone deacetylase
KeywordsHYDROLASE / Deacetylase / Deacylase
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
DECANOIC ACID / IMIDAZOLE / : / Histone deacetylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsGraf, L.G. / Schulze, S. / Palm, G.J. / Lammers, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984/6-1 Germany
German Research Foundation (DFG)LA2984/8-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Distribution and diversity of classical deacylases in bacteria.
Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. ...Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. / Albrecht, D. / Zuhlke, D. / Sievers, S. / Strugnell, R.A. / Olsen, C.A. / Hofmann, K. / Lammers, M.
History
DepositionAug 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone deacetylase
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,80122
Polymers70,5822
Non-polymers1,21920
Water14,250791
1
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,88511
Polymers35,2911
Non-polymers59410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,91511
Polymers35,2911
Non-polymers62410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.11, 51.15, 108.82
Angle α, β, γ (deg.)90, 102.22, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Histone deacetylase


Mass: 35291.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion protein / Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: VN-2825 / Gene: BC353_06500 / Plasmid: pET45-b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A395TF31

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Non-polymers , 6 types, 811 molecules

#2: Chemical ChemComp-DKA / DECANOIC ACID


Mass: 172.265 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 791 / 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: 1.94 Å3/Da / Density % sol: 36.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M Na/K tartrate, 0.1 M imidazole pH 8 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 194694 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 3.45 % / CC1/2: 0.999 / Rrim(I) all: 0.083 / Rsym value: 0.07 / Net I/σ(I): 8.16
Reflection shellResolution: 1.13→1.2 Å / Redundancy: 3.25 % / Mean I/σ(I) obs: 0.65 / Num. unique obs: 29780 / CC1/2: 0.301 / Rrim(I) all: 1.997 / Rsym value: 1.672 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSFeb 5, 2021 BUILT=20210205data reduction
XDSFeb 5, 2021 BUILT=20210205data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.13→46.139 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.9 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1788 9727 4.996 %
Rwork0.1575 184963 -
all0.159 --
obs-194690 94.706 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 17.375 Å2
Baniso -1Baniso -2Baniso -3
1--0.184 Å2-0 Å2-0.325 Å2
2--0.252 Å20 Å2
3---0.067 Å2
Refinement stepCycle: LAST / Resolution: 1.13→46.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4838 0 62 791 5691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0125362
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165069
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.8187337
X-RAY DIFFRACTIONr_angle_other_deg0.6891.74911650
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.367539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.15310877
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.29410258
X-RAY DIFFRACTIONr_chiral_restr0.1060.2806
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.026508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021282
X-RAY DIFFRACTIONr_nbd_refined0.2770.21281
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24554
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22594
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2530
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0690.25
X-RAY DIFFRACTIONr_metal_ion_refined0.2060.240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.250.214
X-RAY DIFFRACTIONr_nbd_other0.1530.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4660.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2190.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.190.21
X-RAY DIFFRACTIONr_mcbond_it1.2761.012613
X-RAY DIFFRACTIONr_mcbond_other1.2661.0092613
X-RAY DIFFRACTIONr_mcangle_it1.9261.8133306
X-RAY DIFFRACTIONr_mcangle_other1.9271.8143307
X-RAY DIFFRACTIONr_scbond_it2.2261.2572749
X-RAY DIFFRACTIONr_scbond_other2.2261.2572750
X-RAY DIFFRACTIONr_scangle_it3.3052.1984005
X-RAY DIFFRACTIONr_scangle_other3.3052.1984006
X-RAY DIFFRACTIONr_lrange_it5.97345.1076557
X-RAY DIFFRACTIONr_lrange_other5.63125.1386271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.13-1.1580.3646650.35712736X-RAY DIFFRACTION88.5958
1.158-1.190.3196640.32912791X-RAY DIFFRACTION90.8385
1.19-1.2250.3256650.30612579X-RAY DIFFRACTION92.4473
1.225-1.2620.2916460.28712244X-RAY DIFFRACTION93.0283
1.262-1.3040.2936230.26712073X-RAY DIFFRACTION93.649
1.304-1.3490.2666260.24811672X-RAY DIFFRACTION94.1366
1.349-1.40.2346110.22811337X-RAY DIFFRACTION95.082
1.4-1.4570.2255690.20811086X-RAY DIFFRACTION95.3998
1.457-1.5220.2165670.18610600X-RAY DIFFRACTION95.8376
1.522-1.5960.1765180.14710229X-RAY DIFFRACTION96.0669
1.596-1.6830.1654710.1399759X-RAY DIFFRACTION96.473
1.683-1.7850.1625120.1299202X-RAY DIFFRACTION96.9461
1.785-1.9080.1474060.1258775X-RAY DIFFRACTION96.8562
1.908-2.060.154410.1278113X-RAY DIFFRACTION97.2377
2.06-2.2560.1484000.127546X-RAY DIFFRACTION97.7608
2.256-2.5220.1383490.1146816X-RAY DIFFRACTION97.6823
2.522-2.9110.1493600.1245996X-RAY DIFFRACTION97.5595
2.911-3.5610.1642860.1295091X-RAY DIFFRACTION96.8829
3.561-5.0210.152330.1184047X-RAY DIFFRACTION99.1429
5.021-46.1390.1491150.1732272X-RAY DIFFRACTION96.9143
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)
10.4529-0.03360.03550.5692-0.15540.5673-0.0103-0.0156-0.0288-0.010.0090.02130.0214-0.01160.00130.02310.0004-0.01750.0230.0020.01775.0652-14.542840.2683
20.4618-0.15490.10270.6275-0.27960.6013-0.0282-0.00730.03980.0522-0.0109-0.0987-0.05590.01520.03910.02090.0028-0.02690.03010.00160.0419-16.00953.614811.5914
Refinement TLS groupSelection: ALL

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