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- PDB-9nns: Flavin-dependent N5-ornithine monooxygenase EtcB -

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Basic information

Entry
Database: PDB / ID: 9nns
TitleFlavin-dependent N5-ornithine monooxygenase EtcB
ComponentsL-lysine N6-monooxygenase MbtG
KeywordsFLAVOPROTEIN / FAD-dependent / erythrochelin / monooxygenase
Function / homologyL-lysine N6-monooxygenase (NADPH) / L-lysine 6-monooxygenase (NADPH) activity / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / biosynthetic process / FAD/NAD(P)-binding domain superfamily / ADENOSINE-5'-DIPHOSPHATE / L-lysine N6-monooxygenase MbtG
Function and homology information
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, Y. / Liu, X. / Smith, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM138396 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)DK042303 United States
CitationJournal: To Be Published
Title: Redefining the Role of the EryM Acetyltransferase in Natural Product Biosynthetic Pathways
Authors: Li, Y. / Liu, X. / Harris, N. / Roberts, J. / Valdivia, E. / Ji, X. / Smith, J.
History
DepositionMar 6, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-lysine N6-monooxygenase MbtG
B: L-lysine N6-monooxygenase MbtG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7884
Polymers101,9332
Non-polymers8542
Water19811
1
A: L-lysine N6-monooxygenase MbtG
B: L-lysine N6-monooxygenase MbtG
hetero molecules

A: L-lysine N6-monooxygenase MbtG
B: L-lysine N6-monooxygenase MbtG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,5758
Polymers203,8664
Non-polymers1,7094
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area12890 Å2
ΔGint-85 kcal/mol
Surface area74110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.725, 83.306, 150.204
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 7 through 60 or (resid 61...
d_2ens_1(chain "B" and (resid 7 through 176 or resid 178...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERGLYGLYAA7 - 18426 - 203
d_12HISHISLEULEUAA189 - 193208 - 212
d_13ARGARGGLYGLYAA207 - 226226 - 245
d_14ALAALAALAALAAA231250
d_15SERSERSERSERAA234253
d_16ASPASPILEILEAA247 - 254266 - 273
d_17VALVALASNASNAA286 - 313305 - 332
d_18LEULEUGLUGLUAA318 - 319337 - 338
d_19ARGARGGLUGLUAA328 - 332347 - 351
d_110LEULEULEULEUAA342361
d_111VALVALTHRTHRAA347 - 432366 - 451
d_112ADPADPADPADPAC501
d_21SERSERASNASNBB7 - 17626 - 195
d_22PROPROGLYGLYBB178 - 226197 - 245
d_23ALAALAALAALABB235254
d_24SERSERSERSERBB238257
d_25ASPASPASNASNBB247 - 313266 - 332
d_26LEULEUGLUGLUBB318 - 332337 - 351
d_27LEULEULEULEUBB334353
d_28VALVALILEILEBB347 - 407366 - 426
d_29LEULEUTHRTHRBB411 - 432430 - 451
d_210ADPADPADPADPBD501

NCS oper: (Code: givenMatrix: (-0.82914827377, -0.0380377190609, 0.557733154862), (0.0353783005046, -0.999252932473, -0.0155548319985), (0.557908160863, 0.0068343890538, 0.829874553875)Vector: 27. ...NCS oper: (Code: given
Matrix: (-0.82914827377, -0.0380377190609, 0.557733154862), (0.0353783005046, -0.999252932473, -0.0155548319985), (0.557908160863, 0.0068343890538, 0.829874553875)
Vector: 27.5403595165, 46.2354554381, -8.4274373526)

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Components

#1: Protein L-lysine N6-monooxygenase MbtG / Lysine 6-N-hydroxylase / Lysine N6-hydroxylase / Lysine-N-oxygenase / Mycobactin synthase protein G


Mass: 50966.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (bacteria) / Gene: SACE_3033 / Production host: Escherichia coli (E. coli)
References: UniProt: A4FE36, L-lysine N6-monooxygenase (NADPH)
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 25% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→41.65 Å / Num. obs: 27141 / % possible obs: 99.86 % / Redundancy: 15.4 % / Biso Wilson estimate: 86.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.982 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2640 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata scaling
PHENIXphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→41.65 Å / SU ML: 0.4969 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.6804
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.35 808 4.07 %
Rwork0.2531 19057 -
obs0.2571 19865 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.74 Å2
Refinement stepCycle: LAST / Resolution: 3→41.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 54 11 5591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00865678
X-RAY DIFFRACTIONf_angle_d1.28717714
X-RAY DIFFRACTIONf_chiral_restr0.0616874
X-RAY DIFFRACTIONf_plane_restr0.0091014
X-RAY DIFFRACTIONf_dihedral_angle_d16.40031997
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 2.67126617402 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.40451300.29483120X-RAY DIFFRACTION99.88
3.19-3.430.34391370.27113129X-RAY DIFFRACTION100
3.43-3.780.35391280.27593149X-RAY DIFFRACTION99.76
3.78-4.330.3751340.23973132X-RAY DIFFRACTION99.57
4.33-5.450.34161380.24553201X-RAY DIFFRACTION99.94
5.45-41.650.33811410.24783326X-RAY DIFFRACTION99.28

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