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- PDB-7qi3: Structure of Fusarium verticillioides NAT1 (FDB2) N-malonyltransferase -

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Basic information

Entry
Database: PDB / ID: 7qi3
TitleStructure of Fusarium verticillioides NAT1 (FDB2) N-malonyltransferase
ComponentsArylamine N-acetyltransferase
KeywordsTRANSFERASE / N-malonyltransferase / N-acetyltransferase / malonyl-CoA / acetyl-CoA / 2-benzoxazolinone
Function / homologyArylamine N-acetyltransferase / N-acetyltransferase / arylamine N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Papain-like cysteine peptidase superfamily / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / N-malonyltransferase FDB2
Function and homology information
Biological speciesFusarium verticillioides (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLowe, E.D. / Kotomina, E. / Karagianni, E. / Boukouvala, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Febs J. / Year: 2023
Title: Fusarium verticillioides NAT1 (FDB2) N-malonyltransferase is structurally, functionally and phylogenetically distinct from its N-acetyltransferase (NAT) homologues.
Authors: Karagianni, E.P. / Kontomina, E. / Lowe, E.D. / Athanasopoulos, K. / Papanikolaou, G. / Garefalaki, V. / Kotseli, V. / Zaliou, S. / Grimaud, T. / Arvaniti, K. / Tsatiri, M.A. / Fakis, G. / ...Authors: Karagianni, E.P. / Kontomina, E. / Lowe, E.D. / Athanasopoulos, K. / Papanikolaou, G. / Garefalaki, V. / Kotseli, V. / Zaliou, S. / Grimaud, T. / Arvaniti, K. / Tsatiri, M.A. / Fakis, G. / Glenn, A.E. / Roversi, P. / Abuhammad, A. / Ryan, A. / Sim, R.B. / Sim, E. / Boukouvala, S.
#1: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2011
Title: Overview of the CCP4 suite and current developments.
Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, ...Authors: Winn, M.D. / Ballard, C.C. / Cowtan, K.D. / Dodson, E.J. / Emsley, P. / Evans, P.R. / Keegan, R.M. / Krissinel, E.B. / Leslie, A.G. / McCoy, A. / McNicholas, S.J. / Murshudov, G.N. / Pannu, N.S. / Potterton, E.A. / Powell, H.R. / Read, R.J. / Vagin, A. / Wilson, K.S.
History
DepositionDec 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arylamine N-acetyltransferase
B: Arylamine N-acetyltransferase
C: Arylamine N-acetyltransferase
D: Arylamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,37020
Polymers158,8484
Non-polymers1,52216
Water25,0411390
1
A: Arylamine N-acetyltransferase
C: Arylamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9919
Polymers79,4242
Non-polymers5677
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint5 kcal/mol
Surface area27510 Å2
MethodPISA
2
B: Arylamine N-acetyltransferase
D: Arylamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,37911
Polymers79,4242
Non-polymers9559
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint13 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.580, 76.880, 92.544
Angle α, β, γ (deg.)76.220, 73.060, 72.490
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Arylamine N-acetyltransferase


Mass: 39712.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusarium verticillioides (fungus)
Gene: FDB2, nat1, FVEG_12636, FVER53263_12636, FVER53590_12636
Production host: Escherichia coli (E. coli) / References: UniProt: B7SP66, arylamine N-acetyltransferase

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Non-polymers , 5 types, 1406 molecules

#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1390 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Morpheus condition H5: 0.1 M amino acids, 0.1 M sodium HEPES/MOPS buffer pH 7.5, 30% PEGMME 550/PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.8→87.32 Å / Num. obs: 160393 / % possible obs: 96.5 % / Redundancy: 1.9 % / Biso Wilson estimate: 23.81 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.4
Reflection shellResolution: 1.8→1.83 Å / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6978 / CC1/2: 0.644

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 1w6f, 1qx3

1w6f

1qx3


Resolution: 1.8→87.32 Å / SU ML: 0.2948 / Cross valid method: FREE R-VALUE / σ(F): 1.95 / Phase error: 26.5623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2216 7755 4.89 %
Rwork0.1784 150916 -
obs0.1805 158671 95.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→87.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10974 0 100 1394 12468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006611825
X-RAY DIFFRACTIONf_angle_d0.82916064
X-RAY DIFFRACTIONf_chiral_restr0.05231735
X-RAY DIFFRACTIONf_plane_restr0.00672110
X-RAY DIFFRACTIONf_dihedral_angle_d15.15584520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.36552790.35554953X-RAY DIFFRACTION93.98
1.82-1.840.35422880.34454914X-RAY DIFFRACTION94.07
1.84-1.860.3472450.3295024X-RAY DIFFRACTION94.95
1.86-1.890.34532600.32025052X-RAY DIFFRACTION94.74
1.89-1.910.32282650.30025045X-RAY DIFFRACTION94.89
1.91-1.940.28152220.2824999X-RAY DIFFRACTION94.89
1.94-1.970.29612740.26355092X-RAY DIFFRACTION94.61
1.97-20.26372750.24894947X-RAY DIFFRACTION95.22
2-2.030.28162690.24315063X-RAY DIFFRACTION95.08
2.03-2.060.25532390.2275018X-RAY DIFFRACTION94.91
2.06-2.10.25992680.2175026X-RAY DIFFRACTION95.34
2.1-2.130.25212600.21035055X-RAY DIFFRACTION95.23
2.13-2.170.27272550.2095004X-RAY DIFFRACTION95.46
2.17-2.220.25762640.20615038X-RAY DIFFRACTION95.39
2.22-2.270.23762740.19065121X-RAY DIFFRACTION95.33
2.27-2.320.25072550.18425047X-RAY DIFFRACTION95.83
2.32-2.380.23652550.17225032X-RAY DIFFRACTION95.36
2.38-2.440.24252720.17345004X-RAY DIFFRACTION95.25
2.44-2.510.23592920.16485047X-RAY DIFFRACTION95.34
2.51-2.60.23382550.16885024X-RAY DIFFRACTION95.13
2.6-2.690.23442380.17015051X-RAY DIFFRACTION94.99
2.69-2.80.2142280.16315050X-RAY DIFFRACTION95
2.8-2.920.21552130.16725059X-RAY DIFFRACTION94.43
2.92-3.080.22442740.16564996X-RAY DIFFRACTION95.04
3.08-3.270.20622830.16225034X-RAY DIFFRACTION95.65
3.27-3.520.18062450.15175093X-RAY DIFFRACTION95.92
3.52-3.880.18042500.14175049X-RAY DIFFRACTION95.2
3.88-4.440.15842240.12595022X-RAY DIFFRACTION94.54
4.44-5.590.17442890.13585054X-RAY DIFFRACTION95.82
5.59-87.320.20332450.17245003X-RAY DIFFRACTION94.27
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)
10.6914363891730.09065698535740.04073384649131.08731446660.2312659460241.411307166230.01661042192010.1248722112090.0303983927036-0.1168269956180.034075440039-0.02551232623480.03206890377770.06949931011750.005859631223170.129184303602-0.00108328812570.01212075585710.139284822548-0.006573200726410.13522097760481.791955046245.775292640127.6745074688
21.625535199080.45514253492-0.8533483426471.20613465943-0.5938714845821.49755759242-0.1580358683930.2803707294310.02893117622-0.09290735375290.12857737249-0.1017306139760.27146641642-0.122674077056-0.01114291308210.15678318938-0.0278564820007-0.02935795888030.150774580469-0.005406100990080.106368330054110.64508457132.832326425563.8227151515
30.85369675887-0.179991753286-0.299600489641.216604929180.311206676511.12401100667-0.0395630782207-0.05735127094310.07720674139690.05616440126490.08885698677970.0630359845696-0.0256755223102-0.07648814639060.00519404011630.1205049412750.00477770346261-0.007064149411390.109751151921-0.0002053128297250.12914353963670.222842167662.613330768656.4544889018
40.9602884728450.292305346974-0.3004611901221.14455111415-0.3601519830851.463645583340.0205262030387-0.08446513209030.05826988856550.1364250429940.05911560378410.0357863413328-0.0242011586718-0.1211927238460.009751207492690.140716317230.01217870790230.01064332513760.151137184593-0.001364845290630.15035670957792.01297977925.556246380592.8823058194
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 5 - 344 / Label seq-ID: 1 - 340

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-ID
11(chain 'A' and resid 5 through 344)AA
22(chain 'B' and resid 5 through 344)BF
33(chain 'C' and resid 5 through 344)CM
44(chain 'D' and resid 5 through 344)DP

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