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- PDB-8heh: Crystal structure of GCN5-related N-acetyltransferase 05790 -

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Basic information

Entry
Database: PDB / ID: 8heh
TitleCrystal structure of GCN5-related N-acetyltransferase 05790
ComponentsGNAT family N-acetyltransferase
KeywordsTRANSFERASE / GNAT 05790
Function / homologyacyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / COENZYME A / GNAT family N-acetyltransferase
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsXu, M.X. / Ran, T.T. / Wang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770074 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2022
Title: Crystal structure of prodigiosin binding protein PgbP, a GNAT family protein, in Serratia marcescens FS14.
Authors: Xu, M. / Liu, X. / Li, X. / Chen, L. / Li, S. / Sun, B. / Xu, D. / Ran, T. / Wang, W.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GNAT family N-acetyltransferase
B: GNAT family N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0255
Polymers37,3982
Non-polymers1,6273
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-13 kcal/mol
Surface area13710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.646, 68.373, 76.012
Angle α, β, γ (deg.)90.000, 98.120, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

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Components

#1: Protein GNAT family N-acetyltransferase


Mass: 18699.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: E4655_15140, FOT62_23610, HMI62_01255 / Production host: Escherichia (bacteria) / References: UniProt: A0A3E2E808
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.4→19.5 Å / Num. obs: 66387 / % possible obs: 100 % / Redundancy: 6.8 % / CC1/2: 0.999 / Net I/σ(I): 19.1
Reflection shellResolution: 1.4→1.48 Å / Num. unique obs: 9608 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
PHENIXv 1.16refinement
XDSdata reduction
SCALAdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→19.5 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2059 --
Rwork0.1857 --
all-66378 -
obs-66387 99.4 %
Displacement parametersBiso mean: 22.33 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 102 207 2613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03262473
X-RAY DIFFRACTIONf_angle_d1.21763355
X-RAY DIFFRACTIONf_chiral_restr0.0915338
X-RAY DIFFRACTIONf_plane_restr0.011424
X-RAY DIFFRACTIONf_dihedral_angle_d20.35831412
LS refinement shellResolution: 1.4→1.48 Å / Num. reflection all: 6597

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