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- PDB-9gn6: Crystal Structure of Deacetylase (HdaH) from Klebsiella pneumonia... -

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Basic information

Entry
Database: PDB / ID: 9gn6
TitleCrystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae in complex with the inhibitor SAHA
ComponentsDeacetylase
KeywordsHYDROLASE / Inhibitor / SAHA / Deacetylase in Complex with SAHA
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
: / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Deacetylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. ozaenae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)42,0255
Polymers41,6171
Non-polymers4084
Water4,179232
1
A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,10020
Polymers166,4694
Non-polymers1,63216
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 area17640 Å2
ΔGint-224 kcal/mol
Surface area42690 Å2
Unit cell
Length a, b, c (Å)146.206, 146.206, 146.206
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

#1: Protein Deacetylase


Mass: 41617.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion-protein
Source: (gene. exp.) Klebsiella pneumoniae subsp. ozaenae (bacteria)
Strain: NCTC10313 / Gene: hdaH, NCTC10313_02007, NCTC5050_05964 / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A377Z5F6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#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-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 2% (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 6, 2019 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.3 Å / Num. obs: 37885 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 41.09 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.02 / Rpim(I) all: 0.02 / Rrim(I) all: 0.028 / Net I/σ(I): 16.3
Reflection shellResolution: 1.95→2 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2642 / CC1/2: 0.532 / Rpim(I) all: 0.597 / Rrim(I) all: 0.844 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSMar 15, 2019 BUILT=20190315data reduction
XDSMar 15, 2019 BUILT=20190315data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.277 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 5.718 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.102
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1756 1859 4.909 %
Rwork0.1373 36012 -
all0.139 --
obs-37871 99.989 %
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: 48.525 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2822 0 22 232 3076
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122914
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162718
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.8143949
X-RAY DIFFRACTIONr_angle_other_deg0.6471.7466256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4555371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.305524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.01710458
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.89110136
X-RAY DIFFRACTIONr_chiral_restr0.0930.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
X-RAY DIFFRACTIONr_nbd_refined0.2380.2639
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22552
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21454
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21596
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2390.2214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0360.22
X-RAY DIFFRACTIONr_metal_ion_refined0.2540.212
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.210
X-RAY DIFFRACTIONr_nbd_other0.1450.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.222
X-RAY DIFFRACTIONr_mcbond_it3.3923.6081481
X-RAY DIFFRACTIONr_mcbond_other3.393.6081481
X-RAY DIFFRACTIONr_mcangle_it4.4576.4541850
X-RAY DIFFRACTIONr_mcangle_other4.4566.4561851
X-RAY DIFFRACTIONr_scbond_it4.5984.0291433
X-RAY DIFFRACTIONr_scbond_other4.5964.0311434
X-RAY DIFFRACTIONr_scangle_it6.3837.1662098
X-RAY DIFFRACTIONr_scangle_other6.3827.1672099
X-RAY DIFFRACTIONr_lrange_it8.75336.0453364
X-RAY DIFFRACTIONr_lrange_other8.63935.1273292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc workWRfactor Rwork
1.95-2.0010.3161260.29526290.29627550.9370.9380.296
2.001-2.0560.281430.25125730.25227160.9480.9590.248
2.056-2.1150.261120.22324840.22525960.9590.9690.215
2.115-2.180.2361040.224900.20125940.9640.9750.187
2.18-2.2510.211240.17223380.17424620.9720.9820.156
2.251-2.330.1791220.15722910.15824130.980.9850.139
2.33-2.4180.2041240.15221610.15522850.9760.9870.132
2.418-2.5160.1741250.14621220.14822470.9830.9890.126
2.516-2.6280.205910.14320580.14521490.9760.990.124
2.628-2.7560.1911050.13519580.13820630.9770.990.119
2.756-2.9040.188860.12918420.13219280.9820.990.117
2.904-3.080.184950.14417750.14618700.9770.9870.135
3.08-3.2910.1971030.14616350.14917380.9740.9870.143
3.291-3.5530.159800.12715640.12816440.9860.990.129
3.553-3.890.181650.12914260.13114910.9790.9910.137
3.89-4.3460.152690.1112960.11213650.9870.9930.124
4.346-5.010.126640.09511490.09612130.9930.9950.111
5.01-6.1190.139450.1149890.11510340.9910.9930.133
6.119-8.5780.194440.1267720.138160.9760.9910.147
8.578-46.2770.13320.1354600.1354920.9890.9870.165
Refinement TLS params.Method: refined / Origin x: -20.0063 Å / Origin y: 8.5714 Å / Origin z: 56.8887 Å
111213212223313233
T0.046 Å20.0285 Å2-0.0376 Å2-0.0527 Å2-0.0052 Å2--0.0413 Å2
L1.1252 °20.1495 °2-0.3322 °2-1.0597 °2-0.2741 °2--0.9705 °2
S-0.0257 Å °0.1494 Å °0.1258 Å °-0.148 Å °-0.0039 Å °0.1458 Å °-0.1049 Å °-0.202 Å °0.0296 Å °
Refinement TLS groupSelection: ALL

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