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- PDB-3ite: The third adenylation domain of the fungal SidN non-ribosomal pep... -

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Basic information

Entry
Database: PDB / ID: 3ite
TitleThe third adenylation domain of the fungal SidN non-ribosomal peptide synthetase
ComponentsSidN siderophore synthetase
KeywordsLIGASE / non-ribosomal peptide synthesis / NRPS / siderophore synthetase / SidNA3 / fungal / endophyte
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / phosphopantetheine binding / ligase activity / metabolic process
Similarity search - Function
ANL, C-terminal domain / ANL, N-terminal domain / Condensation domain / Condensation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site ...ANL, C-terminal domain / ANL, N-terminal domain / Condensation domain / Condensation domain / ANL, N-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nonribosomal peptide synthase sidN
Similarity search - Component
Biological speciesNeotyphodium lolii (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLee, T.V. / Lott, J.S. / Johnson, R.D. / Johnson, L.J. / Arcus, V.L.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis
Authors: Lee, T.V. / Johnson, L.J. / Johnson, R.D. / Koulman, A. / Lane, G.A. / Lott, J.S. / Arcus, V.L.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SidN siderophore synthetase
B: SidN siderophore synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4336
Polymers123,1702
Non-polymers2634
Water8,197455
1
A: SidN siderophore synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7173
Polymers61,5851
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SidN siderophore synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7173
Polymers61,5851
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.598, 75.280, 84.137
Angle α, β, γ (deg.)114.85, 94.78, 90.18
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 13:40 or resseq 46:179 or resseq 183:367 )
211chain B and (resseq 12:40 or resseq 46:180 or resseq 183:367 )
112chain A and (resseq 369:407 )
212chain B and (resseq 369:407 )
113chain A and (resseq 409:421 )
213chain B and (resseq 409:421 )

NCS ensembles :
ID
1
2
3

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Components

#1: Protein SidN siderophore synthetase


Mass: 61585.184 Da / Num. of mol.: 2 / Fragment: Third adenylation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neotyphodium lolii (fungus) / Strain: Lp19 / Gene: sidN / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: K7NCP5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 14% PEG 4000, 0.02 M ammonium sulphate, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97939
SYNCHROTRONSSRL BL9-220.97940, 0.97952, 0.91162
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDDec 17, 2007
MARMOSAIC 325 mm CCD2CCDDec 17, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979391
20.97941
30.979521
40.911621
ReflectionResolution: 2→42.623 Å / Num. obs: 145804 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.084 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 10538 / Rsym value: 0.559 / % possible all: 95

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Processing

Software
NameVersionClassification
Blu-Icedata collection
autoSHARPphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→42.623 Å / FOM work R set: 136.89 / SU ML: 0.27 / Isotropic thermal model: Isotrophic and TLS / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 23.39 / Stereochemistry target values: MLHL
Details: The file contains friedel pairs. The unmerged structure factors for the friedel pairs for each reflection are included under the _refln.pdbx_F_plus and _refln.pdbx_F_minus tags.
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 7343 5.07 %Random
Rwork0.1936 ---
all0.1953 144964 --
obs0.1953 144964 95.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.408 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso mean: 37.225 Å2
Baniso -1Baniso -2Baniso -3
1--8.414 Å21.225 Å22.59 Å2
2---5.63 Å22.387 Å2
3---14.044 Å2
Refinement stepCycle: LAST / Resolution: 2→42.623 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6926 0 12 455 7393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187075
X-RAY DIFFRACTIONf_angle_d1.6459603
X-RAY DIFFRACTIONf_dihedral_angle_d16.822553
X-RAY DIFFRACTIONf_chiral_restr0.0971102
X-RAY DIFFRACTIONf_plane_restr0.0081239
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2657X-RAY DIFFRACTIONPOSITIONAL
12B2657X-RAY DIFFRACTIONPOSITIONAL0.089
21A294X-RAY DIFFRACTIONPOSITIONAL
22B294X-RAY DIFFRACTIONPOSITIONAL0.073
31A100X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.0230.3082430.2974441468494
2.023-2.0470.2762520.2914562481495
2.047-2.0720.3032480.2714472472094
2.072-2.0980.3282600.274612487294
2.098-2.1250.32380.2624408464695
2.125-2.1540.2592080.2534685489395
2.154-2.1850.3032180.2384436465494
2.185-2.2180.2212840.2184616490095
2.218-2.2530.2772520.2484494474695
2.253-2.2890.2772470.2234550479795
2.289-2.3290.262650.2094561482696
2.329-2.3710.242400.2064543478395
2.371-2.4170.2582460.2044661490795
2.417-2.4660.252480.24553480196
2.466-2.520.2032640.1964602486695
2.52-2.5780.2432340.1934519475396
2.578-2.6430.2692860.1894556484296
2.643-2.7140.2252520.1894578483096
2.714-2.7940.262280.1764685491396
2.794-2.8840.2232480.1754599484796
2.884-2.9870.1872110.1654661487296
2.987-3.1070.2172550.164594484997
3.107-3.2480.2032500.1834651490197
3.248-3.420.2012370.1764610484796
3.42-3.6340.1812560.164663491997
3.634-3.9140.232030.1594674487797
3.914-4.3080.1672580.1534626488497
4.308-4.930.1632760.1484619489597
4.93-6.2080.1942070.184710491797
6.208-42.6330.2242290.2074680490997
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)
10.97380.0284-0.07070.4543-0.28590.4165-0.02370.066-0.0126-0.00360.0042-0.03140.0048-0.02320.01480.1279-0.0058-0.00710.1228-0.01140.103633.789135.32665.4474
20.8821-0.1641-0.08230.8240.46220.4765-0.0482-0.0475-0.0384-0.00230.02030.0803-0.00410.02540.02430.13730.00160.00570.11750.01630.147646.2542-2.393679.2091
30.6645-0.236-0.25320.5131-0.20180.0795-0.06870.26810.20830.2320.1909-0.1484-0.4748-0.0922-0.11070.70080.0056-0.06740.42260.06460.393741.831622.0934106.4031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 1-422)A1 - 422
2X-RAY DIFFRACTION2chain B and (resseq 1:421)B1 - 421
3X-RAY DIFFRACTION3chain B and (resseq 422:536)B422 - 536

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