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- PDB-7pk0: Bovine Glycine N-Acyltransferase complexed with Benzoyl-CoA -

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Basic information

Entry
Database: PDB / ID: 7pk0
TitleBovine Glycine N-Acyltransferase complexed with Benzoyl-CoA
ComponentsGlycine N-acyltransferase
KeywordsTRANSFERASE / GLYAT / glycine / benzoyl-CoA / bos taurus / bovine / GNAT
Function / homology
Function and homology information


glycine N-acyltransferase / glycine N-benzoyltransferase / glycine N-acyltransferase activity / glycine N-benzoyltransferase activity / monocarboxylic acid metabolic process / glycine metabolic process / response to toxic substance / mitochondrion
Similarity search - Function
Glycine N-acyltransferase / Glycine N-acyltransferase, C-terminal / Glycine N-acyltransferase, N-terminal / Aralkyl acyl-CoA:amino acid N-acyltransferase / Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / benzoyl coenzyme A / Glycine N-acyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / molecular replacement / Resolution: 1.5 Å
AuthorsOpperman, D.J. / Ebrecht, A.C. / Read, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: To Be Published
Title: Structure of glycine N-acyltransferase clarifies its catalytic mechanism
Authors: Ebrecht, A.C. / Badenhorst, C.P.S. / Read, R.J. / Opperman, D.J. / van Dijk, A.A.
History
DepositionAug 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 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: Glycine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9303
Polymers33,9991
Non-polymers9312
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 63.840, 135.336
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glycine N-acyltransferase / Acyl-CoA:glycine N-acyltransferase / AAc / Aralkyl acyl-CoA N-acyltransferase / Aralkyl acyl-CoA: ...Acyl-CoA:glycine N-acyltransferase / AAc / Aralkyl acyl-CoA N-acyltransferase / Aralkyl acyl-CoA:amino acid N-acyltransferase / Benzoyl-coenzyme A:glycine N-acyltransferase / Glycine N-benzoyltransferase


Mass: 33999.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: GLYAT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2KIR7, glycine N-acyltransferase, glycine N-benzoyltransferase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BYC / benzoyl coenzyme A


Mass: 871.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.03 Å3/Da / Density % sol: 39.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1 M sodium acetate, 30% v/v polyethylene glycol 300, pH 4.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→46.44 Å / Num. obs: 45806 / % possible obs: 99.96 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 15
Reflection shellResolution: 1.5→1.52 Å / Mean I/σ(I) obs: 1.21 / Num. unique obs: 2318 / CC1/2: 0.3 / Rrim(I) all: 2.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.54 Å46.44 Å
Translation5.54 Å46.44 Å

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→46.44 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.914 / SU ML: 0.066 / SU R Cruickshank DPI: 0.0761 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 2291 5 %RANDOM
Rwork0.1808 ---
obs0.1823 43515 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.12 Å2 / Biso mean: 31.1724 Å2 / Biso min: 18.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å2-0 Å2-0 Å2
2--0.65 Å2-0 Å2
3----1.29 Å2
Refinement stepCycle: final / Resolution: 1.5→46.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 60 132 2486
Biso mean--31.07 35.8 -
Num. residues----284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132479
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172308
X-RAY DIFFRACTIONr_angle_refined_deg1.6551.6483374
X-RAY DIFFRACTIONr_angle_other_deg1.4081.5795346
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 1 (DEGREES)6.5385300
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 2 (DEGREES)34.56123.798129
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 3 (DEGREES)12.76115441
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 4 (DEGREES)19.9041510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022814
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
LS refinement shellResolution: 1.5→1.538 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.307 166 -
Rwork0.337 3158 -
obs--99.52 %

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