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- PDB-9gl0: Crystal Structure of Acetylpolyamine aminohydrolase (ApaH) from L... -

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Basic information

Entry
Database: PDB / ID: 9gl0
TitleCrystal Structure of Acetylpolyamine aminohydrolase (ApaH) from Legionella pneumophila
ComponentsAcetylpolyamine aminohydrolase
KeywordsHYDROLASE / Deacetylase / Deacylase
Function / homologyHistone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / hydrolase activity / : / Acetylpolyamine aminohydrolase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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

Downloads & links

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Assembly

Deposited unit
A: Acetylpolyamine aminohydrolase
B: Acetylpolyamine aminohydrolase
C: Acetylpolyamine aminohydrolase
D: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,36510
Polymers201,0254
Non-polymers3406
Water32418
1
A: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3613
Polymers50,2561
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3222
Polymers50,2561
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3613
Polymers50,2561
Non-polymers1052
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Acetylpolyamine aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3222
Polymers50,2561
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.121, 109.121, 400.511
Angle α, β, γ (deg.)90, 90, 90
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein
Acetylpolyamine aminohydrolase


Mass: 50256.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion-protein / Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: LG61 / Gene: C3928_11280 / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2S6EWV0
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M calcium acetate 0.1M Na-HEPES pH 7.5, 18% (w/v) PEG8000

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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: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→45.96 Å / Num. obs: 66768 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 24.7 % / CC1/2: 0.999 / Rrim(I) all: 0.161 / Rsym value: 0.158 / Net I/σ(I): 12.38
Reflection shellResolution: 2.7→2.89 Å / Mean I/σ(I) obs: 0.59 / Num. unique obs: 9462 / CC1/2: 0.673 / % possible all: 87.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSVERSION Jan 10, 2022 BUILT=20220820data reduction
XDSVERSION Jan 10, 2022 BUILT=20220820data scaling
PHASERv3.60.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→45.96 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.316 3279 -
Rwork0.2403 --
obs0.2441 63975 94.56 %
Refinement stepCycle: LAST / Resolution: 2.7→45.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12663 0 6 18 12687
LS refinement shellResolution: 2.7→2.74 Å
RfactorNum. reflection% reflection
Rfree0.6736 45 -
Rwork0.622 --
obs-914 33 %

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