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- PDB-9gn7: Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumonia... -

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Basic information

Entry
Database: PDB / ID: 9gn7
TitleCrystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in Complex with the inhibitor TSA
ComponentsDeacetylase
KeywordsHYDROLASE / Inhibitor / TSA / Deacetylase with TSA
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / PHOSPHATE ION / TRICHOSTATIN A / Deacetylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. ozaenae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsQin, C. / Graf, L.G. / Schulze, S. / Palm, G.J. / Lammers, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984/6-1 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 30, 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
A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3428
Polymers41,6171
Non-polymers7257
Water2,144119
1
A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,36932
Polymers166,4694
Non-polymers2,90128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area21700 Å2
ΔGint-291 kcal/mol
Surface area41780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.57, 146.57, 146.57
Angle α, β, γ (deg.)90, 90, 90
Int Tables number197
Space group name H-MI23
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -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 Deacetylase


Mass: 41617.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-tgged fusion-protein
Source: (gene. exp.) Klebsiella pneumoniae subsp. ozaenae (bacteria)
Strain: NCTC10313 / Gene: hdaH, NCTC10313_02007, NCTC5050_05964 / Plasmid: pET45-b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A377Z5F6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides

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Non-polymers , 6 types, 126 molecules

#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-TSN / TRICHOSTATIN A / 7-[4-(DIMETHYLAMINO)PHENYL]-N-HYDROXY-4,6-DIMETHYL-7-OXO-2,4-HEPTADIENAMIDE


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N2O3 / Feature type: SUBJECT OF INVESTIGATION / Comment: antifungal, antibiotic*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12% (w/v) PEG 8000, 10% (v/v) glycerol and 0.5M KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2019 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.18→47 Å / Num. obs: 27454 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 39.05 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.8
Reflection shellResolution: 2.18→2.25 Å / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2367 / CC1/2: 0.832 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
XDSMar 15, 2019 BUILT=20190315data reduction
XDSMar 15, 2019 BUILT=20190315data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.18→46.393 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.152 / SU B: 4.187 / SU ML: 0.103 / Average fsc free: 0.9728 / Average fsc work: 0.9835 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1862 1378 5.022 %
Rwork0.1478 26059 -
all0.15 --
obs-27437 99.978 %
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: 43.205 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.18→46.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 42 119 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122926
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162720
X-RAY DIFFRACTIONr_angle_refined_deg2.2361.8133963
X-RAY DIFFRACTIONr_angle_other_deg0.7561.7456261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.793528
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00510457
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.48610135
X-RAY DIFFRACTIONr_chiral_restr0.1060.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023545
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.2460.2627
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.22525
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21443
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.21
X-RAY DIFFRACTIONr_metal_ion_refined0.210.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.213
X-RAY DIFFRACTIONr_nbd_other0.1390.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0560.218
X-RAY DIFFRACTIONr_mcbond_it4.9444.0031479
X-RAY DIFFRACTIONr_mcbond_other4.9434.0031479
X-RAY DIFFRACTIONr_mcangle_it6.3927.1491847
X-RAY DIFFRACTIONr_mcangle_other6.3927.1541848
X-RAY DIFFRACTIONr_scbond_it7.2624.6011447
X-RAY DIFFRACTIONr_scbond_other7.2624.6031448
X-RAY DIFFRACTIONr_scangle_it9.2728.1272116
X-RAY DIFFRACTIONr_scangle_other9.278.1282117
X-RAY DIFFRACTIONr_lrange_it10.17237.4073240
X-RAY DIFFRACTIONr_lrange_other10.20237.2633219
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
2.18-2.2370.239880.22119190.22220080.9660.97199.95020.209
2.237-2.2980.2571040.22218720.22419760.9570.971000.206
2.298-2.3640.2251070.20917990.2119060.9680.9741000.194
2.364-2.4370.233890.19517390.19718280.9640.9791000.178
2.437-2.5160.2321030.18216980.18418010.9670.9831000.165
2.516-2.6040.223730.18316620.18517350.9750.9851000.167
2.604-2.7020.236880.15815950.16216830.9660.9861000.144
2.702-2.8120.203790.15115160.15315950.9740.9861000.139
2.812-2.9370.2630.1514820.15215450.9720.9861000.142
2.937-3.080.215780.15814180.16114970.9760.98599.93320.153
3.08-3.2450.226840.16113400.16514240.970.9841000.159
3.245-3.4410.201600.1612600.16213200.9720.9871000.163
3.441-3.6770.179660.15412110.15512770.9820.9881000.16
3.677-3.970.165570.1311280.13111850.9830.9921000.141
3.97-4.3460.13540.10910290.1110830.990.9941000.125
4.346-4.8530.124580.0899340.0919920.9920.9961000.107
4.853-5.5940.167400.1158270.1178670.9880.9941000.133
5.594-6.8260.218250.1627310.1647560.9740.9881000.187
6.826-9.5510.14400.1125560.1145960.990.9931000.143
9.551-46.3930.17220.1633430.1643650.980.9821000.205

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