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- PDB-9gl1: Crystal Structure of Acetylpolyamine aminohydrolase (ApaH) from L... -

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Basic information

Entry
Database: PDB / ID: 9gl1
TitleCrystal Structure of Acetylpolyamine aminohydrolase (ApaH) from Legionella cherrii
ComponentsAcetylpolyamine aminohydrolase
KeywordsHYDROLASE / Deacylase / Deacetylase
Function / homology: / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / histone deacetylase activity / Ureohydrolase domain superfamily / negative regulation of transcription by RNA polymerase II / : / Acetylpolyamine aminohydrolase
Function and homology information
Biological speciesLegionella cherrii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 aminohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2854
Polymers46,1411
Non-polymers1443
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-41 kcal/mol
Surface area15930 Å2
Unit cell
Length a, b, c (Å)113.564, 113.564, 90.426
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Acetylpolyamine aminohydrolase


Mass: 46141.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: His6-tagged truncated (22-409) protein / Source: (gene. exp.) Legionella cherrii (bacteria) / Strain: ORW / Gene: bcp, Lche_0649 / Plasmid: pRSF-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0W0SGS1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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.: 8 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 1 M (NH4)2SO4 5% (w/v) PEG400 0.1 M Na-MES pH 6.5

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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: Sep 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 30383 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 1.4 % / CC1/2: 0.998 / Rsym value: 0.116 / Net I/σ(I): 12.99
Reflection shellResolution: 2.26→2.4 Å / Num. unique obs: 3745 / CC1/2: 0.041 / % possible all: 74

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSJun 30, 2023 BUILT=20230630data reduction
XDSJun 30, 2023 BUILT=20230630data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.2 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2655 1286 -
Rwork0.2373 --
obs0.2388 26323 98.54 %
Refinement stepCycle: LAST / Resolution: 2.4→43.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 3 8 3141
LS refinement shellResolution: 2.4→2.5 Å
RfactorNum. reflection% reflection
Rfree0.527 --
Rwork0.579 --
all-143 -
obs-2704 98 %
Refinement TLS params.Origin x: 4.061 Å / Origin y: -47.5236 Å / Origin z: 9.6132 Å
111213212223313233
T0.7639 Å20.0913 Å2-0.0502 Å2-0.8225 Å20.0552 Å2--0.8194 Å2
L2.1102 °20.683 °20.2104 °2-3.1412 °20.9484 °2--5.4543 °2
S-0.171 Å °0.0646 Å °-0.241 Å °0.0646 Å °0.2862 Å °0.1666 Å °-0.241 Å °0.1666 Å °-0.1079 Å °
Refinement TLS groupSelection details: all

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