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- PDB-9gkv: Crystal Structure of Deacetylase (HdaH) from Vibrio cholerae in c... -

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Basic information

Entry
Database: PDB / ID: 9gkv
TitleCrystal Structure of Deacetylase (HdaH) from Vibrio cholerae in complex with SAHA
ComponentsHistone deacetylase
KeywordsHYDROLASE / Deacetylase / Deacylase / SAHA / Inhibitor
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
ACETATE ION / : / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Histone deacetylase
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGraf, L.G. / Schulze, S. / Lammers, M. / Palm, G.J.
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,40815
Polymers70,5822
Non-polymers82613
Water6,539363
1
B: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7777
Polymers35,2911
Non-polymers4866
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histone deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6318
Polymers35,2911
Non-polymers3407
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.920, 81.530, 133.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 11 - 317 / Label seq-ID: 11 - 317

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules BA

#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: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A395TF31

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 1.97 Å3/Da / Density % sol: 37.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1.4 M sodium acetate 0.1 M MES pH 6.5

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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 PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2024 / Details: mirror
RadiationMonochromator: Silicon111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.9→47.607 Å / Num. obs: 43149 / % possible obs: 96.9 % / Redundancy: 11.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.11 / Net I/σ(I): 12.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2264 / CC1/2: 0.911 / Rpim(I) all: 0.318 / Rrim(I) all: 0.825 / % possible all: 81.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDS30.06.2023data reduction
XDS30.06.2023data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→47.607 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.949 / SU B: 9.117 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.179 / ESU R Free: 0.17
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2403 2162 5.022 %
Rwork0.175 40891 -
all0.178 --
obs-43053 96.644 %
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: 29.447 Å2
Baniso -1Baniso -2Baniso -3
1-2.756 Å20 Å20 Å2
2--0.404 Å20 Å2
3----3.16 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 37 363 5217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0125091
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164742
X-RAY DIFFRACTIONr_angle_refined_deg2.091.8136931
X-RAY DIFFRACTIONr_angle_other_deg0.7191.74510922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9735642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.605537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70310818
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.09210237
X-RAY DIFFRACTIONr_chiral_restr0.1010.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026101
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021175
X-RAY DIFFRACTIONr_nbd_refined0.2650.21227
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.24418
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22497
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.22654
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2327
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2210.22
X-RAY DIFFRACTIONr_metal_ion_refined0.280.232
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2350.233
X-RAY DIFFRACTIONr_nbd_other0.2230.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2640.221
X-RAY DIFFRACTIONr_mcbond_it3.2132.6812537
X-RAY DIFFRACTIONr_mcbond_other3.1732.6812535
X-RAY DIFFRACTIONr_mcangle_it4.4154.7923188
X-RAY DIFFRACTIONr_mcangle_other4.424.7963189
X-RAY DIFFRACTIONr_scbond_it4.3853.0822554
X-RAY DIFFRACTIONr_scbond_other4.3843.0832555
X-RAY DIFFRACTIONr_scangle_it6.2785.4973743
X-RAY DIFFRACTIONr_scangle_other6.2775.4973744
X-RAY DIFFRACTIONr_lrange_it8.69331.2246014
X-RAY DIFFRACTIONr_lrange_other8.63530.5125928
X-RAY DIFFRACTIONr_ncsr_local_group_10.0710.0510528
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BX-RAY DIFFRACTIONLocal ncs0.071090.05008
12AX-RAY DIFFRACTIONLocal ncs0.071090.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.9-1.9490.3441540.31724730.31832490.8870.9180.85570.287
1.949-2.0030.3591420.27925940.28231530.8860.93886.77450.246
2.003-2.0610.3331250.25726680.2630480.9150.95191.63390.221
2.061-2.1240.261540.22327350.22530000.9540.96296.30.186
2.124-2.1930.271390.19627630.229180.9570.97499.45170.16
2.193-2.270.2411350.17226480.17627850.9620.98199.92820.138
2.27-2.3560.2361460.16525670.16927150.9650.98399.92630.133
2.356-2.4520.2511400.18124870.18526310.9640.9899.8480.147
2.452-2.560.2391110.17124060.17425190.9660.98499.92060.139
2.56-2.6850.241290.16622620.1723970.9660.98599.74970.138
2.685-2.830.2091190.15221990.15523180.9770.9871000.13
2.83-3.0010.2431080.17320660.17621740.9660.9821000.152
3.001-3.2070.2671120.18719380.19220560.9620.97999.70820.169
3.207-3.4620.261790.16618100.1718930.9630.98599.78870.159
3.462-3.7910.18870.15116840.15217780.9830.98999.60630.15
3.791-4.2350.193840.13715480.1416370.9810.9999.69460.143
4.235-4.8840.188700.12913560.13214320.9830.99199.5810.145
4.884-5.9660.278620.16711670.17212340.9770.98799.59480.185
5.966-8.3710.194430.1689380.179920.9830.98598.89110.196
8.371-47.6070.28230.1925740.1956020.9610.97499.16940.261
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)
10.20810.0511-0.05990.2030.02920.34990.0020.00820.00380.01760.018-0.011-0.0218-0.0538-0.02010.01080.00860.00630.01370.00370.0068-6.6396-0.0699-29.1223
20.2037-0.02050.21330.09870.05010.5889-0.03020.0035-0.0191-0.00410.029-0.0096-0.0346-0.0170.00120.0152-0.00790.00020.017-0.00610.007318.74560.16380.0085
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLB11 - 401
2X-RAY DIFFRACTION2A9 - 402

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