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- PDB-8osp: GCN5-related N-Acetyltransferase from Lactobacillus curiae -

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Basic information

Entry
Database: PDB / ID: 8osp
TitleGCN5-related N-Acetyltransferase from Lactobacillus curiae
ComponentsN-acetyltransferase
KeywordsTRANSFERASE / GNAT / L curiae / canavanine acetylation / CoA
Function / homology: / acyltransferase activity, transferring groups other than amino-acyl groups / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / PHOSPHATE ION / N-acetyltransferase
Function and homology information
Biological speciesLactobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsFleming, J.R. / Mayans, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: Crystal structure of a GCN5-related N-acetyltransferase from Lactobacillus curiae.
Authors: Fleming, J.R. / Hauth, F. / Hartig, J.S. / Mayans, O.
History
DepositionApr 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-acetyltransferase
C: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,99213
Polymers40,5602
Non-polymers1,43111
Water3,531196
1
A: N-acetyltransferase
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 21.1 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)21,1348
Polymers20,2801
Non-polymers8547
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8585
Polymers20,2801
Non-polymers5784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.680, 37.080, 83.650
Angle α, β, γ (deg.)90.000, 97.670, 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 N-acetyltransferase


Mass: 20280.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus (bacteria) / Gene: PL11_000275 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1S6QFV5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 1 M Potassium sodium tartrate, 0.1 M MES sodium hydroxide pH 6.0

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000021 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000021 Å / Relative weight: 1
ReflectionResolution: 1.95→41.45 Å / Num. obs: 26388 / % possible obs: 96.38 % / Redundancy: 11.54 % / Biso Wilson estimate: 29.54 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.1627 / Net I/σ(I): 10.07
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.9604 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 2286 / CC1/2: 0.77

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.45 Å / SU ML: 0.2007 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9139
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2211 1319 5 %
Rwork0.1827 25057 -
obs0.1846 26376 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.39 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2851 0 88 196 3135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00273006
X-RAY DIFFRACTIONf_angle_d0.6784035
X-RAY DIFFRACTIONf_chiral_restr0.0433420
X-RAY DIFFRACTIONf_plane_restr0.0034505
X-RAY DIFFRACTIONf_dihedral_angle_d15.17371151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.030.27731310.25622486X-RAY DIFFRACTION86.83
2.03-2.120.24631440.21552739X-RAY DIFFRACTION97.4
2.12-2.230.25561490.20442830X-RAY DIFFRACTION98.06
2.23-2.370.2441480.19652809X-RAY DIFFRACTION98.24
2.37-2.560.21871440.19632726X-RAY DIFFRACTION95
2.56-2.810.25261500.19942868X-RAY DIFFRACTION99.21
2.81-3.220.2181520.19182871X-RAY DIFFRACTION98.95
3.22-4.060.20621470.1582794X-RAY DIFFRACTION96.46
4.06-41.450.19991540.16652934X-RAY DIFFRACTION97.47
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.68418527711-0.076390457763-0.08812415607632.3158795602-0.02687645213832.61349302213-0.0276997390802-0.139232666191-0.005765674903030.1831212209410.01282317697220.178642519457-0.0438975669328-0.1097649816420.02418167157040.1579589105590.00936451964048-0.00778620594770.160231248559-0.003029458307330.1809595529517.17734418942.316154345550.670414207595
21.7086685985-0.0706578129862-0.06084868497531.97920596436-0.3099075258612.62633666202-0.0137323837703-0.0503333266538-0.07009271540840.0678041375787-0.03956804478140.1664339338050.0364731606194-0.1522069161750.04195282093340.219857999517-0.0226490467613-0.0006377796141910.150957764849-0.01575165812250.169760492014-1.557025896557.50478168663-30.3349227242
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Label seq-ID: 1

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-ID
11(chain 'A' and resid -2 through 205)AA - C-2 - 205
22(chain 'C' and resid -2 through 202)CE - G-2 - 202

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