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- PDB-9gkz: Crystal Structure of Acetylpolyamine amidohydrolase (ApaH) from P... -

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Basic information

Entry
Database: PDB / ID: 9gkz
TitleCrystal Structure of Acetylpolyamine amidohydrolase (ApaH) from Pseudomonas sp. M30-35
ComponentsAcetylpolyamine amidohydrolase
KeywordsHYDROLASE / Acetylpolyamine amidohydrolase / Polyamine deacetylase / Deacetylase / Deacylase
Function / homology
Function and homology information


histone deacetylase 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 / : / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Acetylpolyamine amidohydrolase
Similarity search - Component
Biological speciesPseudomonas sp. M30-35 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsGraf, L.G. / Schulze, S. / Palm, G.J. / Lammers, M.
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
A: Acetylpolyamine amidohydrolase
B: Acetylpolyamine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,67114
Polymers77,9552
Non-polymers71612
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-107 kcal/mol
Surface area22600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.342, 48.858, 82.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-551-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylpolyamine amidohydrolase


Mass: 38977.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: His6-tagged truncated (1-342) fusion-ptotein / Source: (gene. exp.) Pseudomonas sp. M30-35 (bacteria) / Strain: M30-35 / Gene: B9K09_22070 / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1Y0KY79

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Non-polymers , 7 types, 141 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 1.91 Å3/Da / Density % sol: 35.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M sodium acetate pH 4.5 20% (w/v) PEG3000

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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: 0.97951 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.716→73.671 Å / Num. obs: 16673 / % possible obs: 100 % / Redundancy: 9.3 % / CC1/2: 0.988 / Rmerge(I) obs: 0.237 / Rpim(I) all: 0.081 / Rrim(I) all: 0.251 / Net I/σ(I): 8.9
Reflection shellResolution: 2.716→2.763 Å / Redundancy: 8.6 % / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 795 / CC1/2: 0.731 / Rpim(I) all: 0.372 / Rrim(I) all: 1.092 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSJan 10, 2022 (BUILT 20220220)data reduction
XDSJan 10, 2022 (BUILT 20220220)data scaling
PHASERv3.60.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→73.67 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 833 5 %
Rwork0.1557 --
obs0.1595 16666 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→73.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4974 0 30 129 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085144
X-RAY DIFFRACTIONf_angle_d0.9276993
X-RAY DIFFRACTIONf_dihedral_angle_d6.689707
X-RAY DIFFRACTIONf_chiral_restr0.051728
X-RAY DIFFRACTIONf_plane_restr0.008931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.890.29731230.21632585X-RAY DIFFRACTION100
2.89-3.110.30031400.19892582X-RAY DIFFRACTION100
3.11-3.420.2421530.17932592X-RAY DIFFRACTION100
3.42-3.920.25731210.14292632X-RAY DIFFRACTION100
3.92-4.930.19871350.11962667X-RAY DIFFRACTION100
4.94-73.670.19791610.15042775X-RAY DIFFRACTION100

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