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- PDB-9gn1: Crystal structure of inactive Deacetylase (HdaH) H144A from Klebs... -

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Basic information

Entry
Database: PDB / ID: 9gn1
TitleCrystal structure of inactive Deacetylase (HdaH) H144A from Klebsiella pneumoniae subsp. ozaenae
ComponentsDeacetylase
KeywordsHYDROLASE / Deacetylase / Deacylase / inactive mutant
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
ACETATE ION / IMIDAZOLE / : / Deacetylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. ozaenae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsQin, Q. / 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

Downloads & links

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Assembly

Deposited unit
A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8877
Polymers41,5501
Non-polymers3376
Water2,468137
1
A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules

A: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,54928
Polymers166,2004
Non-polymers1,34924
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 area17220 Å2
ΔGint-350 kcal/mol
Surface area43000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.117, 146.117, 146.117
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: 41550.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion protein, inactive mutant (H144A)
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

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Non-polymers , 5 types, 143 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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 3.13 Å3/Da / Density % sol: 60.68 %
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: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Mar 15, 2019 / Details: mirror
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.35→46.54 Å / Num. obs: 22209 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 20 % / Biso Wilson estimate: 43.14 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.027 / Rrim(I) all: 0.119 / Χ2: 1.1 / Net I/σ(I): 20.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 16.05 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 2147 / CC1/2: 0.913 / Rpim(I) all: 0.21 / Rrim(I) all: 0.978 / Χ2: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
XDSJan 26, 2018data reduction
XDSJan 26, 2018data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→46.249 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.187 / WRfactor Rwork: 0.139 / SU B: 12.721 / SU ML: 0.151 / Average fsc free: 0.966 / Average fsc work: 0.9791 / Cross valid method: FREE R-VALUE / ESU R: 0.214 / ESU R Free: 0.185
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2042 1152 5.296 %
Rwork0.1533 20602 -
all0.156 --
obs-21754 99.972 %
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: 47.322 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.35→46.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2817 0 13 137 2967
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0122891
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162699
X-RAY DIFFRACTIONr_angle_refined_deg2.3041.8143917
X-RAY DIFFRACTIONr_angle_other_deg0.7291.7466209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.165521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89310456
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.55210134
X-RAY DIFFRACTIONr_chiral_restr0.0950.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023512
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02678
X-RAY DIFFRACTIONr_nbd_refined0.260.2654
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.22597
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21423
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2130
X-RAY DIFFRACTIONr_metal_ion_refined0.2350.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0940.211
X-RAY DIFFRACTIONr_nbd_other0.1670.2101
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0460.210
X-RAY DIFFRACTIONr_mcbond_it4.5913.721480
X-RAY DIFFRACTIONr_mcbond_other4.5673.721479
X-RAY DIFFRACTIONr_mcangle_it5.9946.6711847
X-RAY DIFFRACTIONr_mcangle_other5.9936.6731848
X-RAY DIFFRACTIONr_scbond_it5.593.9341411
X-RAY DIFFRACTIONr_scbond_other5.5053.9321410
X-RAY DIFFRACTIONr_scangle_it7.3927.0512070
X-RAY DIFFRACTIONr_scangle_other7.3027.0492068
X-RAY DIFFRACTIONr_lrange_it8.9134.7013252
X-RAY DIFFRACTIONr_lrange_other8.91434.7073253
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
2.35-2.4110.3171000.26314940.26715940.9350.9541000.254
2.411-2.4770.302720.25414730.25615450.9430.9611000.242
2.477-2.5480.301800.24414290.24715090.9450.9631000.229
2.548-2.6270.31650.22913890.23314540.9530.9681000.209
2.627-2.7120.254560.20613720.20814280.960.9761000.181
2.712-2.8070.239490.19313320.19513810.9680.9771000.166
2.807-2.9130.218820.16612300.16913130.9670.98399.92380.139
2.913-3.0310.233600.15412390.15712990.9640.9851000.131
3.031-3.1650.245850.14911340.15612190.9660.9851000.128
3.165-3.3190.189610.13911340.14211950.9780.9881000.121
3.319-3.4980.192490.13110670.13411160.9780.991000.119
3.498-3.7090.163750.1359710.13710460.9850.9911000.126
3.709-3.9630.19660.1269480.1310140.9780.9921000.118
3.963-4.2780.178370.1128850.1149220.9840.9931000.108
4.278-4.6820.174430.1018410.1048840.9860.9941000.1
4.682-5.2280.158400.1217350.1237750.9830.9921000.12
5.228-6.0240.254450.1486530.1556980.9730.9881000.146
6.024-7.3470.233310.1515700.1556010.970.9881000.148
7.347-10.2610.141420.1124280.1154700.9860.9911000.123
10.261-46.2490.146140.2882780.2792930.9890.94999.65870.336
Refinement TLS params.Method: refined / Origin x: -19.9918 Å / Origin y: 8.6121 Å / Origin z: 56.9326 Å
111213212223313233
T0.0355 Å20.0143 Å2-0.0289 Å2-0.0339 Å20.0012 Å2--0.0413 Å2
L1.0424 °2-0.0382 °2-0.464 °2-1.2339 °2-0.3532 °2--0.9208 °2
S-0.0121 Å °0.1047 Å °0.1447 Å °-0.115 Å °-0.0015 Å °0.0687 Å °-0.0816 Å °-0.1241 Å °0.0136 Å °
Refinement TLS groupSelection: ALL

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