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- PDB-8xbp: Crystal structure of AtNATA1 bound to Acetyl CoA -

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Basic information

Entry
Database: PDB / ID: 8xbp
TitleCrystal structure of AtNATA1 bound to Acetyl CoA
ComponentsL-ornithine N5-acetyltransferase NATA1
KeywordsTRANSFERASE / N-amino acetyl transferase
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
ACETYL COENZYME *A / L-ornithine N5-acetyltransferase NATA1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsHameed, U.F.S. / Arold, S.T.
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 Acetyl CoA
Authors: Hameed, U.F.S. / Arold, S.T.
History
DepositionDec 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 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)50,6847
Polymers48,9452
Non-polymers1,7395
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.290, 50.780, 60.210
Angle α, β, γ (deg.)90.00, 92.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein L-ornithine N5-acetyltransferase NATA1


Mass: 24472.266 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
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.49 Å3/Da / Density % sol: 50.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium acetate tetrahydrate, 0.1 M Sodium cacodylate pH 6.5, and 20% w/v PEG 8000.

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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: Jun 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.99→47.7 Å / Num. obs: 28289 / % possible obs: 91.8 % / Redundancy: 6.4 % / CC1/2: 0.99 / Net I/σ(I): 7.44
Reflection shellResolution: 1.99→2.06 Å / Num. unique obs: 7554 / CC1/2: 0.23

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→47.7 Å / SU B: 16.685 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28828 1415 5 %RANDOM
Rwork0.25032 ---
obs0.25217 26874 91.87 %-
Displacement parametersBiso mean: 24.635 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å2-0.1 Å2
2--0.42 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 105 154 3485
LS refinement shellResolution: 1.99→2.06 Å

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