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- PDB-8xbn: Crystal structure of Arabidopsis N-amino acetyltransferase NATA1 ... -

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Basic information

Entry
Database: PDB / ID: 8xbn
TitleCrystal structure of Arabidopsis N-amino acetyltransferase NATA1 bound to CoA and HEPES
ComponentsL-ornithine N5-acetyltransferase NATA1
KeywordsTRANSFERASE / Acetyltransferase / acetylation
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 N5-acetyltransferase NATA1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 Arabidopsis NATA1 bound to CoA and HEPES
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
C: L-ornithine N5-acetyltransferase NATA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9566
Polymers48,9452
Non-polymers2,0124
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-33 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.320, 76.620, 82.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


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, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#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.: 271 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Magnesium chloride hexahydrate, 0.1 M Sodium HEPES pH 7.5, and 10% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.35→42.28 Å / Num. obs: 88772 / % possible obs: 98.63 % / Redundancy: 13.2 % / CC1/2: 0.99 / Net I/σ(I): 19.54
Reflection shellResolution: 1.35→1.39 Å / Num. unique obs: 8164 / CC1/2: 0.41

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Processing

Software
NameVersionClassification
REFMAC5.5refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→42.28 Å / SU B: 2.989 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.053 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18379 4439 5 %RANDOM
Rwork0.15608 ---
obs0.15746 84333 99.2 %-
Displacement parametersBiso mean: 27.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0 Å2-0 Å2
2--0.13 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.35→42.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 63 271 3710

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