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- PDB-7pk2: Bovine Glycine N-Acyltransferase -

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Basic information

Entry
Database: PDB / ID: 7pk2
TitleBovine Glycine N-Acyltransferase
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-benzoyltransferase activity / glycine N-acyltransferase activity / glycine metabolic process / monocarboxylic acid 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
MALONATE ION / Glycine N-acyltransferase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.25 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

Downloads & links

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Assembly

Deposited unit
A: Glycine N-acyltransferase
B: Glycine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2024
Polymers67,9982
Non-polymers2042
Water7,800433
1
A: Glycine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1012
Polymers33,9991
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycine N-acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1012
Polymers33,9991
Non-polymers1021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.112, 63.587, 135.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2
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-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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 Å3/Da / Density % sol: 38.48 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium malonate, 20% w/v polyethylene glycol 3,350, pH 5.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
1931N
2451N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONDiamond I0310.9762
SYNCHROTRONDiamond I2322.755
Detector
TypeIDDetectorDate
DECTRIS EIGER2 X 16M1PIXELOct 15, 2020
DECTRIS PILATUS 12M2PIXELMay 18, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97621
22.7551
Reflection

Entry-ID: 7PK2 / CC1/2: 1

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRpim(I) allRrim(I) allDiffraction-IDNet I/σ(I)
1.25-37.3714694797.226.80.0430.0180.047116.2
1.8-58.0948496866.5211.5
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID
1.25-1.251.1866250.41
1.8-1.830.816750.42

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.45 Å37.37 Å
Translation4.45 Å37.37 Å

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Processing

Software
NameVersionClassification
xia2data reduction
XSCALEdata scaling
SHELXDphasing
CRANK2phasing
HKL2Mapmodel building
PHASER2.8.3phasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.25→37.37 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.065 / SU ML: 0.043 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.05 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 7348 5 %RANDOM
Rwork0.1768 ---
obs0.1779 139600 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.47 Å2 / Biso mean: 23.2609 Å2 / Biso min: 12.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.88 Å2-0 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.25→37.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 14 433 5035
Biso mean--20.24 29.78 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135024
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174771
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.6416864
X-RAY DIFFRACTIONr_angle_other_deg1.451.57811086
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 1 (DEGREES)6.5215656
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 2 (DEGREES)34.10923.612263
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 3 (DEGREES)13.85315942
X-RAY DIFFRACTIONTORSION ANGLES. PERIOD 4 (DEGREES)20.5821524
X-RAY DIFFRACTIONr_chiral_restr0.0920.2640
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021165
LS refinement shellResolution: 1.25→1.282 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 507 -
Rwork0.337 9634 -
all-10141 -
obs--91.87 %

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