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- PDB-8gxk: Pseudomonas jinjuensis N-acetyltransferase -

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Basic information

Entry
Database: PDB / ID: 8gxk
TitlePseudomonas jinjuensis N-acetyltransferase
ComponentsProtein N-acetyltransferase, RimJ/RimL family
KeywordsTRANSFERASE / Complex with AcCoA / ACETYLTRANSFERASE
Function / homologyAcetyltransferase (GNAT) domain / N-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / COENZYME A / Protein N-acetyltransferase, RimJ/RimL family
Function and homology information
Biological speciesPseudomonas jinjuensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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

Downloads & links

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Assembly

Deposited unit
A: Protein N-acetyltransferase, RimJ/RimL family
B: Protein N-acetyltransferase, RimJ/RimL family
C: Protein N-acetyltransferase, RimJ/RimL family
D: Protein N-acetyltransferase, RimJ/RimL family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4618
Polymers85,3904
Non-polymers3,0704
Water7,278404
1
A: Protein N-acetyltransferase, RimJ/RimL family
B: Protein N-acetyltransferase, RimJ/RimL family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2304
Polymers42,6952
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein N-acetyltransferase, RimJ/RimL family
D: Protein N-acetyltransferase, RimJ/RimL family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2304
Polymers42,6952
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.876, 100.687, 94.618
Angle α, β, γ (deg.)90.000, 96.199, 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
Protein N-acetyltransferase, RimJ/RimL family


Mass: 21347.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas jinjuensis (bacteria) / Gene: SAMN05216193_102137 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H0A919
#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.: 404 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1M Tris-HCl pH8.5, 15%PEG6000, 0.2M NaCl

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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: Mar 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.78→33.43 Å / Num. obs: 75982 / % possible obs: 99.76 % / Redundancy: 5.6 % / Biso Wilson estimate: 18.48 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 21.8
Reflection shellResolution: 1.78→1.84 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 7475

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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: 1.78→33.43 Å / SU ML: 0.1979 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.6881 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.247 1999 2.63 %
Rwork0.205 73911 -
obs0.206 75910 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.29 Å2
Refinement stepCycle: LAST / Resolution: 1.78→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5916 0 192 404 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01456233
X-RAY DIFFRACTIONf_angle_d2.01118465
X-RAY DIFFRACTIONf_chiral_restr0.1076908
X-RAY DIFFRACTIONf_plane_restr0.01131091
X-RAY DIFFRACTIONf_dihedral_angle_d31.60262403
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.31541400.21655181X-RAY DIFFRACTION98.77
1.83-1.880.28171420.22025261X-RAY DIFFRACTION100
1.88-1.930.3341420.25485262X-RAY DIFFRACTION99.98
1.93-1.990.2911430.21735281X-RAY DIFFRACTION99.94
1.99-2.060.22811430.20295297X-RAY DIFFRACTION99.83
2.06-2.150.24721430.20315287X-RAY DIFFRACTION100
2.15-2.250.28581430.21045262X-RAY DIFFRACTION99.98
2.25-2.360.26581430.21725292X-RAY DIFFRACTION99.98
2.36-2.510.25591420.20365286X-RAY DIFFRACTION99.98
2.51-2.710.2711430.21595289X-RAY DIFFRACTION99.96
2.71-2.980.25931420.22565261X-RAY DIFFRACTION100
2.98-3.410.22591440.21085311X-RAY DIFFRACTION99.91
3.41-4.290.22941450.18225351X-RAY DIFFRACTION99.96
4.29-33.430.20041440.18465290X-RAY DIFFRACTION98.58
Refinement TLS params.Method: refined / Origin x: 3.9712283414 Å / Origin y: 12.4043505511 Å / Origin z: 24.219588318 Å
111213212223313233
T0.048452153555 Å2-0.00381992075479 Å27.89068365046E-5 Å2-0.0406855896902 Å2-0.00137197962785 Å2--0.0433908440033 Å2
L0.049633202628 °2-0.0192233204061 °2-0.0120595800315 °2--0.0199309553396 °20.0358803279051 °2--0.0616216305901 °2
S0.005274190185 Å °-0.00591904094335 Å °0.00242152017849 Å °-0.00211152970156 Å °0.00737925744984 Å °0.000401729500409 Å °0.00573434379557 Å °0.00550462876314 Å °-2.11631918453E-13 Å °
Refinement TLS groupSelection details: all

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