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

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Basic information

Entry
Database: PDB / ID: 9glb
TitleCrystal Structure of Deacetylase (HdaH) from Klebsiella pneumoniae subsp. ozaenae
ComponentsDeacetylase
KeywordsHYDROLASE / Deacetylase / Deacylase
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 / : / Deacetylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. ozaenae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 27, 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
C: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9517
Polymers41,6171
Non-polymers3346
Water4,306239
1
C: Deacetylase
hetero molecules

C: Deacetylase
hetero molecules

C: Deacetylase
hetero molecules

C: Deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,80428
Polymers166,4694
Non-polymers1,33524
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
Unit cell
Length a, b, c (Å)147.163, 147.163, 147.163
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
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
Components on special symmetry positions
IDModelComponents
11C-647-

HOH

21C-814-

HOH

31C-839-

HOH

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Components

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Protein , 1 types, 1 molecules C

#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

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Non-polymers , 5 types, 245 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 3.19 Å3/Da / Density % sol: 61.45 %
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
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: 2.1→46.54 Å / Num. obs: 31019 / % possible obs: 100 % / Redundancy: 19.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.033 / Rrim(I) all: 0.148 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 20.5 % / Rmerge(I) obs: 2.755 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2547 / CC1/2: 0.549 / Rpim(I) all: 0.622 / Rrim(I) all: 2.824 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSJan 26, 2018 BUILT=20180808data reduction
XDSJan 26, 2018 BUILT=20180808data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→26.01 Å / SU ML: 0.2057 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.0604
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1806 1587 5.12 %
Rwork0.151 29387 -
obs0.1525 30974 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.14 Å2
Refinement stepCycle: LAST / Resolution: 2.1→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2818 0 14 239 3071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00712892
X-RAY DIFFRACTIONf_angle_d0.83213919
X-RAY DIFFRACTIONf_chiral_restr0.0468417
X-RAY DIFFRACTIONf_plane_restr0.0081527
X-RAY DIFFRACTIONf_dihedral_angle_d6.2668402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.26831650.25372646X-RAY DIFFRACTION99.96
2.17-2.250.27071440.22352632X-RAY DIFFRACTION99.96
2.25-2.340.21011250.20452679X-RAY DIFFRACTION99.96
2.34-2.440.24671460.18642640X-RAY DIFFRACTION99.93
2.44-2.570.21591430.18352655X-RAY DIFFRACTION100
2.57-2.730.21431400.17162665X-RAY DIFFRACTION100
2.73-2.940.19661370.1742675X-RAY DIFFRACTION100
2.94-3.240.20271260.16682672X-RAY DIFFRACTION100
3.24-3.70.17841520.14282676X-RAY DIFFRACTION100
3.7-4.660.14491530.12082694X-RAY DIFFRACTION100
4.66-26.010.1581560.12992753X-RAY DIFFRACTION99.22
Refinement TLS params.Method: refined / Origin x: -19.7683637341 Å / Origin y: 8.61903929484 Å / Origin z: 57.9130814502 Å
111213212223313233
T0.367132730311 Å20.0461717092379 Å2-0.103053631413 Å2-0.414479395568 Å2-0.0528404759552 Å2--0.429923390295 Å2
L0.932840588346 °20.242009431572 °2-0.20903372692 °2-1.18530270182 °20.0172708795547 °2--1.15818969053 °2
S-0.0551693729191 Å °0.18146960947 Å °0.117528392481 Å °-0.217358674469 Å °-0.0582723529786 Å °0.279009609565 Å °-0.137221843058 Å °-0.245151794699 Å °0.111419350401 Å °
Refinement TLS groupSelection details: all

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