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- PDB-6yzz: Arabidopsis thaliana Naa50 in complex with AcCoA -

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Basic information

Entry
Database: PDB / ID: 6yzz
TitleArabidopsis thaliana Naa50 in complex with AcCoA
ComponentsN-alpha-acetyltransferase 50
KeywordsTRANSFERASE / N-alpha-acetyltransferase / GNAT-fold / Naa50 / Arabidopsis thaliana
Function / homology
Function and homology information


: / seedling development / : / NatA complex / peptide alpha-N-acetyltransferase activity / root development / cell death / N-acetyltransferase activity / mitotic sister chromatid cohesion / response to endoplasmic reticulum stress ...: / seedling development / : / NatA complex / peptide alpha-N-acetyltransferase activity / root development / cell death / N-acetyltransferase activity / mitotic sister chromatid cohesion / response to endoplasmic reticulum stress / endoplasmic reticulum / nucleus / cytoplasm / cytosol
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 / Acyl-CoA N-acyltransferases (NAT) superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWeidenhausen, J. / Kopp, J. / Lapouge, K. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)SI 586/6-1 Germany
German Research Foundation (DFG)201348542 - SFB 1036(TP22) Germany
CitationJournal: Structure / Year: 2021
Title: Structural and functional characterization of the N-terminal acetyltransferase Naa50.
Authors: Weidenhausen, J. / Kopp, J. / Armbruster, L. / Wirtz, M. / Lapouge, K. / Sinning, I.
History
DepositionMay 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 19, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-alpha-acetyltransferase 50
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2132
Polymers19,4031
Non-polymers8101
Water1,54986
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, SEC-MALS: protein elutes as a monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-3 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.164, 100.164, 100.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Space group name HallI223
Symmetry operation#1: x,y,z
#2: z,x,y
#3: y,z,x
#4: -y,-z,x
#5: z,-x,-y
#6: -y,z,-x
#7: -z,-x,y
#8: -z,x,-y
#9: y,-z,-x
#10: x,-y,-z
#11: -x,y,-z
#12: -x,-y,z
#13: x+1/2,y+1/2,z+1/2
#14: z+1/2,x+1/2,y+1/2
#15: y+1/2,z+1/2,x+1/2
#16: -y+1/2,-z+1/2,x+1/2
#17: z+1/2,-x+1/2,-y+1/2
#18: -y+1/2,z+1/2,-x+1/2
#19: -z+1/2,-x+1/2,y+1/2
#20: -z+1/2,x+1/2,-y+1/2
#21: y+1/2,-z+1/2,-x+1/2
#22: x+1/2,-y+1/2,-z+1/2
#23: -x+1/2,y+1/2,-z+1/2
#24: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-386-

HOH

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Components

#1: Protein N-alpha-acetyltransferase 50 / At5g11340 / Separation anxiety protein-like


Mass: 19403.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g11340, F2I11.230, F2I11_230 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q9LFM3
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.16 Å3/Da / Density % sol: 43.08 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 34 mg mL-1 protein (20 mM HEPES pH 8.0, 250 mM NaCl) mixed with AcCoA (5.4 mM); drops (600 nL): 1:1 mix of (20 mM HEPES pH 8.0, 250 mM NaCl) and (0.9 M sodium citrate, 0.1 M sodium ...Details: 34 mg mL-1 protein (20 mM HEPES pH 8.0, 250 mM NaCl) mixed with AcCoA (5.4 mM); drops (600 nL): 1:1 mix of (20 mM HEPES pH 8.0, 250 mM NaCl) and (0.9 M sodium citrate, 0.1 M sodium cacodylate pH 6.5). Growth after 19 h, 20 % glycerol (v/v) as cryo protection

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0781 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.79→40.89 Å / Num. obs: 16046 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 33.54 Å2 / CC1/2: 1 / Rpim(I) all: 0.019 / Net I/σ(I): 21.2
Reflection shellResolution: 1.79→1.82 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 914 / CC1/2: 0.616 / Rpim(I) all: 0.752 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSVERSION Nov 11, 2017 BUILT=20171111data reduction
Aimless7.0.073data scaling
Coot0.8.9.2model building
PHASER1.17.1_3660phasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ob0

2ob0


Resolution: 1.79→40.89 Å / SU ML: 0.1925 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4281
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.197 852 5.31 %
Rwork0.1699 15184 -
obs0.1713 16036 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.85 Å2
Refinement stepCycle: LAST / Resolution: 1.79→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 51 86 1344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691286
X-RAY DIFFRACTIONf_angle_d0.92121745
X-RAY DIFFRACTIONf_chiral_restr0.0572192
X-RAY DIFFRACTIONf_plane_restr0.0042215
X-RAY DIFFRACTIONf_dihedral_angle_d16.6939469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.90.32531470.2582492X-RAY DIFFRACTION99.85
1.9-2.040.26271390.22232512X-RAY DIFFRACTION100
2.04-2.250.26041030.19372550X-RAY DIFFRACTION100
2.25-2.570.21451380.18872528X-RAY DIFFRACTION99.89
2.58-3.240.18731650.18782508X-RAY DIFFRACTION99.93
3.25-40.890.16921600.14212594X-RAY DIFFRACTION99.75
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.6029710084-0.4567282815232.930321690576.74676019202-2.140250002642.126653929820.4125690004131.00147859123-0.264711360195-1.48949433739-0.2094558337270.417499765491.006463356460.1959875343690.02444255761760.4739563331860.01994633508090.02153096143320.385765716489-0.06989056891820.259942696416-11.90050518121.4632462512-5.47102541358
25.668226579270.9733828370741.014071496582.16332948721-0.5535151819873.92869311648-0.07479537043280.1473163939220.072754178248-0.179123418058-0.0250450465036-0.142266295844-0.1325780943020.2533759931490.09149256700570.2428295774140.03072925951930.02993466758450.2120029662580.00381808274430.192685693607-7.875396581824.81197856784.60578463913
310.02681454333.75626159782-7.285222010025.40713911108-3.571034584499.16929449980.206218139525-0.6932337441010.2681798112660.360932390475-0.1862659794070.129493955971-0.3187276404710.755213373354-0.1984922245140.2563881857160.00147924845978-0.03720051039980.2918020910530.01364315861350.193425138814-15.401627458725.3200193925.00850747291
43.32741644894.59321256316-0.7812647227627.93394800082-3.550066046854.048148950220.162511331911-0.5558931653170.7925313411320.336294548394-0.1378107226010.738770902697-0.236586936647-0.0712801807866-0.1349269201580.2852832215170.0368849877675-0.002726098248830.291120084175-0.06685144356230.3115842773-22.899030519727.158230798510.2597538366
59.347249507372.22598826177-2.668014018542.53112069505-1.794379776963.54264235518-0.1108527185831.116927661950.262435727811-0.3613203021210.09823630057030.0356735718447-0.0832154532758-0.1815139831040.02194296417990.352035643461-0.0026757382191-0.05334644197630.3487028665130.04109854426960.227894936936-17.405310314829.443084627-4.66549500188
66.871046886253.194404900044.055838823042.627354845655.556802930838.80439958664-0.248240972774-0.03716955933580.9378690652950.324768064537-0.0265795945250.768491601371-0.4441936117030.1379448197730.2794671040810.2624930004360.0270501822515-0.03339256685010.209743078209-0.0001778784235080.298974834376-23.549319491632.89319893878.33828290349
72.225546919544.220291563435.005403182492.101276993541.756659239742.21298815953-0.5405406989220.9582645106551.43185643991-0.820757439690.08204887618870.430051886825-1.406328186160.5469186596050.4376440509990.601653690215-0.0205719104977-0.06266106966070.4899829487410.1301647082740.552275549515-21.190142326341.07347671880.0733057705887
82.225022720550.7113764653231.973902085692.208378146011.890435463662.13418247711-0.270116878383-0.246355798690.6168754001460.217746337685-0.1265736661150.948873976187-1.05148861502-0.8092960965930.8734954868780.5136144593180.114059099958-0.04303973217740.452977613154-0.04545082099320.543830469052-27.15410865539.76112519229.70379189997
92.05721405129-0.905869275885.277811408465.20405085039-3.551026919894.332039298860.3899150359440.11980987509-0.107220112916-0.337263495575-0.0404841594929-0.9348108141390.08486600799161.05004711044-0.3791108574580.4724052663930.0770002274153-0.1057567677740.552020047735-0.1903275446860.609842398254-13.678633690340.640578299318.2557447157
106.406459456592.654019307384.134932499836.444287295883.621553113072.45202227325-0.237262847361-0.4342781772830.02772999853120.04526338322760.1212853838850.151069198638-0.4127876335-0.513195040881-0.02926468597930.380160386204-0.0165592974362-0.07191572883620.3269141280270.01106561183320.413945379175-26.676293848236.12852934497.90414350142
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 83 )
5X-RAY DIFFRACTION5chain 'A' and (resid 84 through 106 )
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 120 )
7X-RAY DIFFRACTION7chain 'A' and (resid 121 through 130 )
8X-RAY DIFFRACTION8chain 'A' and (resid 131 through 138 )
9X-RAY DIFFRACTION9chain 'A' and (resid 139 through 149 )
10X-RAY DIFFRACTION10chain 'A' and (resid 150 through 157 )

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