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- PDB-8gxj: Pseudomonas aeruginosa N-acetyltransferase domain-containing prot... -

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Basic information

Entry
Database: PDB / ID: 8gxj
TitlePseudomonas aeruginosa N-acetyltransferase domain-containing protein PA3270
ComponentsN-acetyltransferase domain-containing protein
KeywordsTRANSFERASE / Apo-form of PA3270 / 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 / N-acetyltransferase domain-containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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 1.3Nov 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

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Assembly

Deposited unit
A: N-acetyltransferase domain-containing protein
B: N-acetyltransferase domain-containing protein
C: N-acetyltransferase domain-containing protein
D: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)87,7214
Polymers87,7214
Non-polymers00
Water1,67593
1
A: N-acetyltransferase domain-containing protein
C: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)43,8602
Polymers43,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-1 kcal/mol
Surface area17890 Å2
MethodPISA
2
B: N-acetyltransferase domain-containing protein

D: N-acetyltransferase domain-containing protein


Theoretical massNumber of molelcules
Total (without water)43,8602
Polymers43,8602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+3/41
Buried area2160 Å2
ΔGint0 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.250, 100.250, 147.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein
N-acetyltransferase domain-containing protein


Mass: 21930.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA3270 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HYX1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1% n-Octyl-D-glucoside, 0.1M Sodium citrate pH 5.5, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→17.41 Å / Num. obs: 74789 / % possible obs: 99.69 % / Redundancy: 13.68 % / Biso Wilson estimate: 39.34 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 39.34
Reflection shellResolution: 2.18→2.26 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 5420 / % possible all: 99.95

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000v1.0data reduction
HKL-2000v1.0data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YRE

1yre


Resolution: 2.18→17.41 Å / SU ML: 0.271 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5673 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.254 3744 5.01 %
Rwork0.2084 71045 -
obs0.2108 74789 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.01 Å2
Refinement stepCycle: LAST / Resolution: 2.18→17.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5901 0 0 93 5994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01066023
X-RAY DIFFRACTIONf_angle_d1.15758163
X-RAY DIFFRACTIONf_chiral_restr0.0646898
X-RAY DIFFRACTIONf_plane_restr0.00591072
X-RAY DIFFRACTIONf_dihedral_angle_d27.90842266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.210.33321370.29852593X-RAY DIFFRACTION99.85
2.21-2.240.33851380.28662632X-RAY DIFFRACTION99.75
2.24-2.270.33911360.28352626X-RAY DIFFRACTION99.93
2.27-2.30.33311410.2722637X-RAY DIFFRACTION99.96
2.3-2.330.33411420.26852665X-RAY DIFFRACTION99.96
2.33-2.370.28461350.2592592X-RAY DIFFRACTION100
2.37-2.410.27861320.2442663X-RAY DIFFRACTION100
2.41-2.450.29081400.24332596X-RAY DIFFRACTION99.96
2.45-2.490.26631420.24192663X-RAY DIFFRACTION100
2.49-2.540.32241350.2412602X-RAY DIFFRACTION100
2.54-2.590.28931420.24062638X-RAY DIFFRACTION99.96
2.59-2.650.31391380.23522644X-RAY DIFFRACTION100
2.65-2.710.28651360.23122675X-RAY DIFFRACTION100
2.71-2.780.28951400.22842613X-RAY DIFFRACTION100
2.78-2.850.28541360.23432620X-RAY DIFFRACTION100
2.85-2.940.27631390.22352633X-RAY DIFFRACTION100
2.94-3.030.31621320.22892648X-RAY DIFFRACTION100
3.03-3.140.29251380.22162634X-RAY DIFFRACTION100
3.14-3.270.30121390.22092618X-RAY DIFFRACTION100
3.27-3.410.26311380.20292644X-RAY DIFFRACTION99.93
3.41-3.590.26381440.21062624X-RAY DIFFRACTION100
3.59-3.810.20071430.18872620X-RAY DIFFRACTION99.96
3.81-4.10.22451440.17622631X-RAY DIFFRACTION99.96
4.1-4.510.22771380.16372627X-RAY DIFFRACTION99.93
4.51-5.150.19821340.172637X-RAY DIFFRACTION100
5.15-6.430.29461460.22512638X-RAY DIFFRACTION99.93
6.43-17.410.17671390.1772632X-RAY DIFFRACTION99.86

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