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- PDB-8xj5: Crystal structure of AtNATA1 bound to Ornithine and CoA -

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Basic information

Entry
Database: PDB / ID: 8xj5
TitleCrystal structure of AtNATA1 bound to Ornithine and CoA
ComponentsL-ornithine N5-acetyltransferase NATA1
KeywordsTRANSFERASE / Acetyltransferase / acetylation / polyamines
Function / homology
Function and homology information


ornithine metabolic process / response to jasmonic acid / N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / defense response
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
COENZYME A / L-ornithine / L-ornithine N5-acetyltransferase NATA1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsArold, S.T. / Hameed, U.F.S.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other privateKing Abdullah University of Science and Technology Saudi Arabia
CitationJournal: To Be Published
Title: Crystal structure of AtNATA1 bound to Ornithine and CoA
Authors: Arold, S.T. / Hameed, U.F.S.
History
DepositionDec 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ornithine N5-acetyltransferase NATA1
Q: L-ornithine N5-acetyltransferase NATA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7346
Polymers46,9342
Non-polymers1,7994
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-61 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.040, 74.070, 110.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein L-ornithine N5-acetyltransferase NATA1 / Protein N-ACETYLTRANSFERASE ACTIVITY 1


Mass: 23467.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NATA1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9ZV05, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.92 Å3/Da / Density % sol: 36.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Lithium sulfate, 0.1 M BIS-Tris pH 5.5, and 25% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.04→42.53 Å / Num. obs: 24570 / % possible obs: 99.4 % / Redundancy: 13.3 % / CC1/2: 0.99 / CC star: 0.99 / Net I/σ(I): 8.13
Reflection shellResolution: 2.04→2.11 Å / Num. unique obs: 2288 / CC1/2: 0.49 / % possible all: 94.12

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→42.53 Å / SU B: 14.755 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.239 / ESU R Free: 0.198 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25102 2000 8.1 %RANDOM
Rwork0.19993 ---
obs0.20405 22570 99.35 %-
Displacement parametersBiso mean: 31.769 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.06 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.04→42.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 96 61 3180

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