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- PDB-6z00: Arabidopsis thaliana Naa50 in complex with bisubstrate analogue C... -

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Basic information

Entry
Database: PDB / ID: 6z00
TitleArabidopsis thaliana Naa50 in complex with bisubstrate analogue CoA-Ac-MVNAL
Components
  • Acyl-CoA N-acyltransferases (NAT) superfamily protein
  • MET-VAL-ASN-ALA-LEU
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
CARBOXYMETHYL COENZYME *A / Acyl-CoA N-acyltransferases (NAT) superfamily protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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 1.3May 1, 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

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Assembly

Deposited unit
A: Acyl-CoA N-acyltransferases (NAT) superfamily protein
B: Acyl-CoA N-acyltransferases (NAT) superfamily protein
C: MET-VAL-ASN-ALA-LEU
D: MET-VAL-ASN-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5516
Polymers39,9004
Non-polymers1,6512
Water4,612256
1
A: Acyl-CoA N-acyltransferases (NAT) superfamily protein
C: MET-VAL-ASN-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7763
Polymers19,9502
Non-polymers8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-10 kcal/mol
Surface area8220 Å2
MethodPISA
2
B: Acyl-CoA N-acyltransferases (NAT) superfamily protein
D: MET-VAL-ASN-ALA-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7763
Polymers19,9502
Non-polymers8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-9 kcal/mol
Surface area8300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.863, 73.862, 74.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Acyl-CoA N-acyltransferases (NAT) superfamily protein / At5g11340 / Separation anxiety protein-like


Mass: 19403.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: DOM = CoA-Ac-MVNAL; SMILES: O[C@H](C(C)(COP(OP(OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C2N=CN=C3N)O)OP([O-])(O)=O)([O-])=O)([O-])=O)C)C(NCCC(NCCSCC(N[C@@H](CCSC)C(N[C@H](C(N[C@H](C(N[C@H] ...Details: DOM = CoA-Ac-MVNAL; SMILES: O[C@H](C(C)(COP(OP(OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C2N=CN=C3N)O)OP([O-])(O)=O)([O-])=O)([O-])=O)C)C(NCCC(NCCSCC(N[C@@H](CCSC)C(N[C@H](C(N[C@H](C(N[C@H](C(N[C@@H](CC(C)C)C(O)=O)=O)C)=O)CC(N)=O)=O)C(C)C)=O)=O)=O)=O
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: Protein/peptide MET-VAL-ASN-ALA-LEU


Mass: 546.680 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-CMC / CARBOXYMETHYL COENZYME *A


Mass: 825.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O18P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 32.5 mg mL-1 protein mixed with CoA-Ac-MVNAL (2.5 mM); drops (400 nL): 1:1 mix of (20 mM HEPES pH 8.0, 250 mM NaCl) and (1 M LiCl, 10 % (w/v) PEG 6000, 0.1 M citric acid pH 4.0). Crystals ...Details: 32.5 mg mL-1 protein mixed with CoA-Ac-MVNAL (2.5 mM); drops (400 nL): 1:1 mix of (20 mM HEPES pH 8.0, 250 mM NaCl) and (1 M LiCl, 10 % (w/v) PEG 6000, 0.1 M citric acid pH 4.0). Crystals after 20 h; 20 % (v/v) glycerol as cryo protectant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.983997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2019 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983997 Å / Relative weight: 1
ReflectionResolution: 1.42→47.62 Å / Num. obs: 64831 / % possible obs: 99.48 % / Redundancy: 12.8 % / Biso Wilson estimate: 17.94 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.032 / Net I/σ(I): 13.3
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 12.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3133 / CC1/2: 0.529 / Rpim(I) all: 0.622 / % possible all: 98.8

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Processing

Software
NameVersionClassification
XDSVERSION Mar 15, 2019 BUILT=20190606data reduction
Aimless7.0.073data scaling
PHASER1.17.1_3660phasing
Coot0.8.9.2model building
PHENIX1.18_3845refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AtNaa50/AcCoA

Resolution: 1.42→47.62 Å / SU ML: 0.1486 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.5875
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1914 3255 5.02 %
Rwork0.1635 61567 -
obs0.1641 64822 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.37 Å2
Refinement stepCycle: LAST / Resolution: 1.42→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2447 0 176 256 2879
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172714
X-RAY DIFFRACTIONf_angle_d1.07213686
X-RAY DIFFRACTIONf_chiral_restr0.0793403
X-RAY DIFFRACTIONf_plane_restr0.0051456
X-RAY DIFFRACTIONf_dihedral_angle_d20.8851983
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.27321320.2452614X-RAY DIFFRACTION98.42
1.44-1.460.27821210.22842624X-RAY DIFFRACTION98.49
1.46-1.490.27241390.22422621X-RAY DIFFRACTION98.96
1.49-1.510.251210.20862667X-RAY DIFFRACTION99.29
1.51-1.540.25161400.18532633X-RAY DIFFRACTION99.07
1.54-1.570.21831350.17352640X-RAY DIFFRACTION99
1.57-1.60.20711480.16812629X-RAY DIFFRACTION99.21
1.6-1.640.22321670.15592612X-RAY DIFFRACTION99.21
1.64-1.680.21451380.16182655X-RAY DIFFRACTION99.5
1.68-1.720.22471120.15022700X-RAY DIFFRACTION99.5
1.72-1.760.17731320.15022669X-RAY DIFFRACTION99.61
1.76-1.820.18021550.14342640X-RAY DIFFRACTION99.64
1.82-1.870.18061970.14582615X-RAY DIFFRACTION99.54
1.87-1.940.1751490.14472656X-RAY DIFFRACTION99.86
1.94-2.020.16471460.14242676X-RAY DIFFRACTION99.65
2.02-2.110.19151380.14292675X-RAY DIFFRACTION99.79
2.11-2.220.17691420.14432705X-RAY DIFFRACTION99.93
2.22-2.360.18431340.15362693X-RAY DIFFRACTION100
2.36-2.540.18871430.16172726X-RAY DIFFRACTION100
2.54-2.80.2071230.17442723X-RAY DIFFRACTION100
2.8-3.20.20321200.1712780X-RAY DIFFRACTION99.97
3.21-4.040.16661540.15792739X-RAY DIFFRACTION99.55
4.04-47.620.18421690.16882875X-RAY DIFFRACTION99.84

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