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

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Basic information

Entry
Database: PDB / ID: 6tgx
TitleCrystal structure of Arabidopsis thaliana NAA60 in complex with a bisubstrate analogue
Components
  • Acyl-CoA N-acyltransferases (NAT) superfamily protein
  • MET-VAL-ASN-ALA
KeywordsPLANT PROTEIN / N-alpha-acetyltransferase NAA60 NatF NAT
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
CARBOXYMETHYL COENZYME *A / histone acetyltransferase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 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

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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
C: MET-VAL-ASN-ALA
D: MET-VAL-ASN-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0886
Polymers42,4374
Non-polymers1,6512
Water3,297183
1
A: Acyl-CoA N-acyltransferases (NAT) superfamily protein
C: MET-VAL-ASN-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0443
Polymers21,2182
Non-polymers8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-9 kcal/mol
Surface area9250 Å2
MethodPISA
2
B: Acyl-CoA N-acyltransferases (NAT) superfamily protein
D: MET-VAL-ASN-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0443
Polymers21,2182
Non-polymers8261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-9 kcal/mol
Surface area9210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.062, 76.165, 109.226
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 / 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: Protein/peptide MET-VAL-ASN-ALA


Mass: 433.522 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 / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: reservoir: 0.1 M citric acid pH 5 and 20 % (w/v) PEG 6000 protein: c=13mg/ml drop: 200nl protein solution + 200 nl precipitant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 1.77→45.51 Å / Num. obs: 41529 / % possible obs: 99.84 % / Redundancy: 12.5 % / Biso Wilson estimate: 33.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Net I/σ(I): 14.9
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 12.7 % / Rmerge(I) obs: 2.414 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2329 / CC1/2: 0.511 / Rpim(I) all: 0.7 / % 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: D_1292105306

Resolution: 1.77→45.51 Å / SU ML: 0.2233 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.7465
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.218 2101 5.07 %
Rwork0.1806 39335 -
obs0.1825 41436 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.18 Å2
Refinement stepCycle: LAST / Resolution: 1.77→45.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2810 0 158 183 3151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01073035
X-RAY DIFFRACTIONf_angle_d0.98984115
X-RAY DIFFRACTIONf_chiral_restr0.0623445
X-RAY DIFFRACTIONf_plane_restr0.0062513
X-RAY DIFFRACTIONf_dihedral_angle_d16.63551728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.34471250.29682579X-RAY DIFFRACTION99.78
1.81-1.860.33751540.27552597X-RAY DIFFRACTION99.96
1.86-1.910.29171510.26092557X-RAY DIFFRACTION99.74
1.91-1.960.25281370.24272550X-RAY DIFFRACTION99.48
1.96-2.030.26421420.22292620X-RAY DIFFRACTION99.93
2.03-2.10.26491400.21242570X-RAY DIFFRACTION99.85
2.1-2.180.23941400.1932633X-RAY DIFFRACTION100
2.18-2.280.22751430.2022589X-RAY DIFFRACTION99.78
2.28-2.40.28641200.19292620X-RAY DIFFRACTION99.96
2.4-2.550.22041390.19852612X-RAY DIFFRACTION99.82
2.55-2.750.25681290.19462618X-RAY DIFFRACTION100
2.75-3.030.2461400.18812655X-RAY DIFFRACTION100
3.03-3.460.19831480.17852642X-RAY DIFFRACTION99.96
3.46-4.360.18761340.15052702X-RAY DIFFRACTION99.96
4.36-45.510.18831590.15742791X-RAY DIFFRACTION99.53
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)
14.36196806879-0.6061203707810.7384102429547.16129616216-0.6871839221375.60410436829-0.0523030851364-0.1427503290740.35425671353-0.1585884627260.189220951479-0.0544629561682-0.7251284545920.00836152972001-0.0399625023220.416701200538-0.04880240931260.02602562691960.256305444756-0.02366117300410.270454679581-30.7772075152101.51331941623.3053218408
27.756398584460.541632024568-1.453600628069.94513578623-4.815373236395.375614245830.04819080524580.255825448060.491600123949-0.3099470326560.000984929692645-0.755349242516-0.6582472477550.735186094177-0.05216129785870.562043109109-0.1485056050230.07956920535460.403326940893-0.08227240370130.355690636359-22.212516839597.085422047117.5733386112
33.33220577989-0.08361089673560.1460419108735.54580323561.815389953281.215355406460.0287314667005-0.1584818301070.527961598084-0.3742138985430.2788542029470.129193220346-1.25785997350.0809904983453-0.4608983606050.486174236997-0.0462415521429-0.007139853630830.3389418691090.03742668253550.366770343285-33.9161274106100.70909693117.8408163415
44.28004480462-2.735084759054.341434294769.77644964761-1.674983225216.041983497570.823668483351.774039808750.293134576533-1.45444767203-0.4357815001260.529940001298-0.2076556281.26563749997-0.3743633357710.77984372402-0.0591658035038-0.03671813542680.73707265855-0.05744852526330.491371920298-34.291100064986.1798967774-4.40723635542
52.674563556770.3912094625550.5052755695433.870521224612.525958031086.514433707220.09845893599770.112700503025-0.224600859265-0.4195124689690.1193529960220.1279988621270.0499029048093-0.107787151544-0.2113591626050.319392647574-0.0708835759658-0.05832356157920.2769832016010.02317044936910.306847851927-35.552452895386.538648511113.3836307617
66.032316591191.955680549482.176343574242.814758908480.02399193701646.09242876336-0.1887250643070.3368190195410.142799070783-0.01018728898150.0176025990336-0.0880887802833-0.1866364025820.29347008450.220230137510.245374715197-0.01098992857570.0110079787150.255204663529-0.00321306671120.247586758021-22.85377968496.371904409539.5447017973
75.362944310485.112902546534.849265257314.956155019294.191343637787.660004454930.0203813597516-0.02216070265011.091523467590.194761197589-0.3217966900890.793121846851-0.427193375547-0.646570815460.327975372160.3199810030220.04616624699060.01728525572260.346791634937-0.02137469714690.364161295538-31.2160239927100.72330410745.6700964594
86.58188535836-0.343238707149-0.4855177168295.815521549341.255684972028.175284727280.01136468804880.5272162005070.0637414342384-0.5321820644440.256613845389-0.765638121658-0.2693429121251.18995720264-0.315102693260.31692624566-0.1087908849470.0320138288980.449315048664-0.01263518571350.479448217164-17.390014660693.550297690639.123099861
93.773692890570.958031020043-3.568542693511.14434786745-1.327515511513.566198485710.283600569845-0.3293908199460.1643414734830.155381130716-0.0851947818101-0.0116329758462-0.583056353050.266821592271-0.2249517931810.31080879415-0.00741064878145-0.03678170690180.326533741853-0.01689757760490.28214351128-28.223488484791.370834023353.5112882657
105.814682313691.051910669396.888832060267.633610502721.546968742438.773441579880.195937862402-0.0838585815789-0.7082161309730.884065077076-0.1282253049710.2541753507310.4354798871870.840825613716-0.1961548285620.4307372281160.1064634033820.05826263619850.4818712126860.06812870163850.239497869271-33.955403141884.03882532466.8332602225
112.255858856170.1949860651590.523966669252.647975515230.3937156257289.12985840291-0.0215430103848-0.0976494643627-0.142513970692-0.076504822414-0.0669825797551-0.2823065053350.3547055056220.242912308890.08755615629940.1653511084950.01839611307580.02116911896260.2407377703270.03573127374530.279778583478-24.86178911784.937560463245.5736746177
124.03517395014-0.007996755939040.4441862202873.74025514921-0.04781277916567.36287332073-0.212129965401-0.068424439698-0.3870811442580.0205564206631-0.00261916405324-0.004847689223970.189683498480.1334597761650.1445941096360.179861827564-0.01439797031270.07966155205920.2019853669250.00811406710560.245289169425-33.367198806981.439772927849.1560891046
137.75595405675-2.37968716918-0.3832389200554.32749502263-2.846986064057.44038400852-0.08812522393180.0742734919043-0.1917190956630.009216091507980.148352394620.2754536582820.0853221649696-0.24355626057-0.1532044451320.228905618796-0.03906186763870.0289155416230.228771316789-0.02442657846150.237286509068-40.570374487383.918417458750.0214855878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 95 )
4X-RAY DIFFRACTION4chain 'A' and (resid 96 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 200 )
6X-RAY DIFFRACTION6chain 'B' and (resid 24 through 45 )
7X-RAY DIFFRACTION7chain 'B' and (resid 46 through 60 )
8X-RAY DIFFRACTION8chain 'B' and (resid 61 through 81 )
9X-RAY DIFFRACTION9chain 'B' and (resid 82 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 111 )
11X-RAY DIFFRACTION11chain 'B' and (resid 112 through 144 )
12X-RAY DIFFRACTION12chain 'B' and (resid 145 through 168 )
13X-RAY DIFFRACTION13chain 'B' and (resid 169 through 198 )

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