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- PDB-6th0: Crystal structure of Arabidopsis thaliana NAA60 in complex with a... -

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Basic information

Entry
Database: PDB / ID: 6th0
TitleCrystal structure of Arabidopsis thaliana NAA60 in complex with acetyl-CoA
ComponentsAcyl-CoA N-acyltransferases (NAT) superfamily protein
KeywordsPLANT PROTEIN / N-alpha-acetyltransferase NAA60 acetyl-CoA NatF
Function / homology
Function and homology information


peptide alpha-N-acetyltransferase activity / histone acetyltransferase / chromosome segregation
Similarity search - Function
N-alpha-acetyltransferase 60-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / histone acetyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLayer, D. / Kopp, J. / Lapouge, K. / Sinning, I.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCollaborative Research Centre 1036 Germany
Other privateLeibniz Programme Germany
CitationJournal: New Phytol. / Year: 2020
Title: The Arabidopsis N alpha -acetyltransferase NAA60 locates to the plasma membrane and is vital for the high salt stress response.
Authors: Linster, E. / Layer, D. / Bienvenut, W.V. / Dinh, T.V. / Weyer, F.A. / Leemhuis, W. / Brunje, A. / Hoffrichter, M. / Miklankova, P. / Kopp, J. / Lapouge, K. / Sindlinger, J. / Schwarzer, D. ...Authors: Linster, E. / Layer, D. / Bienvenut, W.V. / Dinh, T.V. / Weyer, F.A. / Leemhuis, W. / Brunje, A. / Hoffrichter, M. / Miklankova, P. / Kopp, J. / Lapouge, K. / Sindlinger, J. / Schwarzer, D. / Meinnel, T. / Finkemeier, I. / Giglione, C. / Hell, R. / Sinning, I. / Wirtz, M.
History
DepositionNov 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 16, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acyl-CoA N-acyltransferases (NAT) superfamily protein
B: Acyl-CoA N-acyltransferases (NAT) superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1894
Polymers41,5702
Non-polymers1,6192
Water1,58588
1
A: Acyl-CoA N-acyltransferases (NAT) superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5942
Polymers20,7851
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Acyl-CoA N-acyltransferases (NAT) superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5942
Polymers20,7851
Non-polymers8101
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.147, 71.997, 77.926
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU(chain 'A' and (resid 24 through 182 or resid 185 through 197))AA24 - 1825 - 163
12GLYGLYILEILE(chain 'A' and (resid 24 through 182 or resid 185 through 197))AA185 - 197166 - 178
23THRTHRLEULEUchain 'B'BB24 - 1825 - 163
24GLYGLYILEILEchain 'B'BB185 - 197166 - 178

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Components

#1: Protein Acyl-CoA N-acyltransferases (NAT) superfamily protein / At5g16800


Mass: 20784.869 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g16800, F5E19.140, F5E19_140 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta II (DE3) / References: UniProt: Q6NLS5
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: reservoir: 0.1 M HEPES pH 7.5, 100 mM NaCl and 1.1 M NH4SO4 protein sample: c = 5 mg/ml drop composition: volume: 250 nl protein solution + 250 nl precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.999998 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999998 Å / Relative weight: 1
ReflectionResolution: 1.75→42.01 Å / Num. obs: 39965 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 36.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Net I/σ(I): 16.9
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.036 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2180 / CC1/2: 0.756 / Rpim(I) all: 0.581 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
Cootmodel building
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ICV

5icv


Resolution: 1.75→42.01 Å / SU ML: 0.2246 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.6047
RfactorNum. reflection% reflection
Rfree0.2255 2137 5.37 %
Rwork0.2019 37675 -
obs0.2033 39812 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.67 Å2
Refinement stepCycle: LAST / Resolution: 1.75→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 102 88 3016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772997
X-RAY DIFFRACTIONf_angle_d0.98064065
X-RAY DIFFRACTIONf_chiral_restr0.0673438
X-RAY DIFFRACTIONf_plane_restr0.007507
X-RAY DIFFRACTIONf_dihedral_angle_d16.19171733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.45091220.40772492X-RAY DIFFRACTION99.77
1.79-1.840.34971210.35052490X-RAY DIFFRACTION99.09
1.84-1.890.34941090.29932490X-RAY DIFFRACTION99.35
1.89-1.940.25381390.26632471X-RAY DIFFRACTION99.54
1.94-20.281590.24782472X-RAY DIFFRACTION99.32
2-2.070.27781160.23482495X-RAY DIFFRACTION99.54
2.07-2.160.29621590.22062461X-RAY DIFFRACTION99.81
2.16-2.260.26681560.21422483X-RAY DIFFRACTION99.7
2.26-2.380.24221560.21542490X-RAY DIFFRACTION99.85
2.38-2.520.23581330.23022514X-RAY DIFFRACTION99.96
2.52-2.720.28251370.22332515X-RAY DIFFRACTION100
2.72-2.990.24961290.21192557X-RAY DIFFRACTION100
2.99-3.430.21721410.20382549X-RAY DIFFRACTION100
3.43-4.310.2121820.17682527X-RAY DIFFRACTION99.93
4.31-42.010.18661780.17242669X-RAY DIFFRACTION99.86
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)
16.337307566971.184028900540.2834903738945.13803434951-0.5939635804427.00659084230.171649125646-0.6695565640790.6574240736430.548572628824-0.1334072176120.0403580847299-0.6628152451520.606749589562-0.05833702802170.356354210589-0.08038273246870.01729761368380.442980261564-0.09025620874070.38375815282265.093090767184.41537876825.9711243315
26.13796990966-1.6220170266-1.881354292541.290724234910.4151973772813.437253896460.0133580885192-0.1809294752230.264609759107-0.101685448840.130494919403-0.252138377742-0.2147984433661.11700246161-0.1684134765350.348190824925-0.0892156585484-0.007052571295620.5711831132930.02615025842080.32065683277573.975771444379.009800523212.4777610585
36.191402919182.2988037997-4.167226176018.1225170705-2.450757006838.11333773783-0.224534040193-0.0632285237858-0.0199269461172-0.1213779077490.07032305348460.06137109871910.0780944012130.595289711220.18448753750.2858437437610.0359241691663-0.07850787569330.3476164422250.02340860562890.19497559457167.070089147171.40966479538.03221495285
46.67488780495-0.3848881833894.06599829533.02986585176-1.132799710655.920527773320.1525725508350.0548666919972-0.4772798238610.07382943700660.1005893528250.1433842514160.2641377401840.249289139018-0.2119098063570.3509078431360.01974389893690.03029284938120.3118639238830.04517408834220.37135157277158.897342987562.7946237363-6.17672675181
50.7073843107281.11839035311.039009146113.888420617350.04732387862342.72038388426-0.331956223789-1.35717156494-0.2257252886570.4072365434470.3826511941980.17784477104-0.06701076171350.4735535017390.2544013948340.2840535840140.03091067765530.0003359541408450.5517194730560.08175987020960.23837789794464.043053568165.3961005184-5.94687985598
64.43644770680.309793413396-0.1804438512541.264566723290.8738671818841.06073914556-0.2939718332870.2568904522830.104239272137-0.04179434610650.211609255036-0.276033358518-0.1602890601271.18639609747-0.01938901909740.331051017426-0.07029616562620.01703392639530.8533423047980.09117516855290.38843803860172.79743112769.5270009419-10.9007290135
76.568303938490.0717377997459-0.7830807290463.712081991940.8576870270454.67109529789-0.07585005223761.54644299699-0.587924959555-0.498608996016-0.216722359870.1110523482810.05735263195140.1010242912590.3697076429490.405082807296-0.04103060190670.007170159763381.33010528476-0.02905784215210.47742447056273.45933169865.7928310013-20.7144583177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 199 )
4X-RAY DIFFRACTION4chain 'B' and (resid 24 through 75 )
5X-RAY DIFFRACTION5chain 'B' and (resid 76 through 95 )
6X-RAY DIFFRACTION6chain 'B' and (resid 96 through 144 )
7X-RAY DIFFRACTION7chain 'B' and (resid 145 through 197 )

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