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- PDB-7qi3: Structure of Fusarium verticillioides NAT1 (FDB2) N-malonyltransferase -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qi3 | ||||||
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Title | Structure of Fusarium verticillioides NAT1 (FDB2) N-malonyltransferase | ||||||
![]() | Arylamine N-acetyltransferase | ||||||
![]() | TRANSFERASE / N-malonyltransferase / N-acetyltransferase / malonyl-CoA / acetyl-CoA / 2-benzoxazolinone | ||||||
Function / homology | Arylamine 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lowe, E.D. / Kotomina, E. / Karagianni, E. / Boukouvala, S. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 716.3 KB | Display | ![]() |
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PDB format | ![]() | 494.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 487.1 KB | Display | ![]() |
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Full document | ![]() | 493.7 KB | Display | |
Data in XML | ![]() | 62.9 KB | Display | |
Data in CIF | ![]() | 94.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1qx3S ![]() 1w6fS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 39712.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: FDB2, nat1, FVEG_12636, FVER53263_12636, FVER53590_12636 Production host: ![]() ![]() |
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-Non-polymers , 5 types, 1406 molecules ![](data/chem/img/PEG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PGE / | #5: Chemical | ChemComp-PG4 / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: Ensemble of 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→87.32 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth seq-ID: 5 - 344 / Label seq-ID: 1 - 340
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