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- PDB-8gxf: Pseudomonas flexibilis GCN5 family acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 8gxf
TitlePseudomonas flexibilis GCN5 family acetyltransferase
ComponentsGCN5 family acetyltransferase
KeywordsTRANSFERASE / Complex with AcCoA / Acetyltransferase
Function / homologyAcetyltransferase (GNAT) domain / acyltransferase activity, transferring groups other than amino-acyl groups / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / COENZYME A / GCN5 family acetyltransferase
Function and homology information
Biological speciesPseudomonas flexibilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsSong, Y.J. / Bao, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81871615 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: The novel type II toxin-antitoxin PacTA modulates Pseudomonas aeruginosa iron homeostasis by obstructing the DNA-binding activity of Fur.
Authors: Song, Y. / Zhang, S. / Ye, Z. / Song, Y. / Chen, L. / Tong, A. / He, Y. / Bao, R.
History
DepositionSep 20, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GCN5 family acetyltransferase
A: GCN5 family acetyltransferase
C: GCN5 family acetyltransferase
D: GCN5 family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9958
Polymers87,9254
Non-polymers3,0704
Water66737
1
B: GCN5 family acetyltransferase
A: GCN5 family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4974
Polymers43,9622
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-1 kcal/mol
Surface area17630 Å2
MethodPISA
2
C: GCN5 family acetyltransferase
D: GCN5 family acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4974
Polymers43,9622
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1640 Å2
ΔGint-4 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.889, 99.013, 98.822
Angle α, β, γ (deg.)90.000, 101.866, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
GCN5 family acetyltransferase / Protein N-acetyltransferase / RimJ/RimL family


Mass: 21981.154 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas flexibilis (bacteria) / Gene: PT85_02890, SAMN05421672_12249 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B3C4T8
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M NaCl, 0.1M MES pH6.5, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.04→42.95 Å / Num. obs: 30921 / % possible obs: 99.6 % / Redundancy: 9.4 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.471 / Net I/σ(I): 34.1
Reflection shellResolution: 3.04→3.15 Å / Rmerge(I) obs: 0.511 / Num. unique obs: 15925

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
PHENIX1.20.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRE

1yre


Resolution: 3.04→42.95 Å / SU ML: 0.4601 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.4492 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.3019 3093 10 %
Rwork0.225 27828 -
obs0.2328 30921 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.64 Å2
Refinement stepCycle: LAST / Resolution: 3.04→42.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6020 0 192 37 6249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02196332
X-RAY DIFFRACTIONf_angle_d2.10378588
X-RAY DIFFRACTIONf_chiral_restr0.1051916
X-RAY DIFFRACTIONf_plane_restr0.01621112
X-RAY DIFFRACTIONf_dihedral_angle_d33.85642452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.04-3.090.36241440.26231197X-RAY DIFFRACTION92.93
3.09-3.140.37051380.28271259X-RAY DIFFRACTION97.01
3.14-3.20.33961350.27671278X-RAY DIFFRACTION97.99
3.2-3.250.36041550.26131201X-RAY DIFFRACTION98.91
3.25-3.320.3521320.23861279X-RAY DIFFRACTION99.3
3.32-3.390.33011350.24581308X-RAY DIFFRACTION99.38
3.39-3.460.371440.24611240X-RAY DIFFRACTION99.78
3.46-3.540.35141410.22851241X-RAY DIFFRACTION99.57
3.54-3.630.29221450.2331312X-RAY DIFFRACTION99.39
3.63-3.730.33411350.23051228X-RAY DIFFRACTION99.49
3.73-3.840.31581380.22731309X-RAY DIFFRACTION100
3.84-3.960.29191520.211289X-RAY DIFFRACTION99.86
3.96-4.10.26021390.18841263X-RAY DIFFRACTION100
4.1-4.260.24211450.18181276X-RAY DIFFRACTION99.79
4.26-4.460.29111350.19671269X-RAY DIFFRACTION99.36
4.46-4.690.22981460.1851280X-RAY DIFFRACTION99.72
4.69-4.990.29421400.19641249X-RAY DIFFRACTION99.86
4.99-5.370.28851410.2271279X-RAY DIFFRACTION99.93
5.37-5.910.29831290.24431284X-RAY DIFFRACTION100
5.91-6.760.29081460.2521264X-RAY DIFFRACTION99.79
6.76-8.510.27371410.22811288X-RAY DIFFRACTION99.79
8.51-42.950.26731370.23061235X-RAY DIFFRACTION96.96

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