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- PDB-6x0j: Structure of reduced SidA ornithine hydroxylase with the FAD "in"... -

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Basic information

Entry
Database: PDB / ID: 6x0j
TitleStructure of reduced SidA ornithine hydroxylase with the FAD "in" and complexed with NADP and L-ornithine
ComponentsL-ornithine N(5)-monooxygenase
KeywordsOXIDOREDUCTASE / FLAVIN-CONTAINING MONOOXYGENASE / FLAVOPROTEIN
Function / homology
Function and homology information


L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / NADP+ binding / secondary metabolite biosynthetic process ...L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / siderophore-dependent iron import into cell / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / ergosterol biosynthetic process / NADP+ binding / secondary metabolite biosynthetic process / monooxygenase activity / intracellular iron ion homeostasis / iron ion binding
Similarity search - Function
L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-ornithine / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.335 Å
AuthorsTanner, J.J. / Campbell, A.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2003658 United States
National Science Foundation (NSF, United States)CHE-2003986 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Trapping conformational states of a flavin-dependent N -monooxygenase in crystallo reveals protein and flavin dynamics.
Authors: Campbell, A.C. / Stiers, K.M. / Martin Del Campo, J.S. / Mehra-Chaudhary, R. / Sobrado, P. / Tanner, J.J.
History
DepositionMay 15, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ornithine N(5)-monooxygenase
B: L-ornithine N(5)-monooxygenase
C: L-ornithine N(5)-monooxygenase
D: L-ornithine N(5)-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,56316
Polymers223,9104
Non-polymers6,65312
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23790 Å2
ΔGint-129 kcal/mol
Surface area70100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.208, 153.015, 91.114
Angle α, β, γ (deg.)90.000, 110.910, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 31 through 36 or (resid 37...
21(chain B and (resid 31 through 36 or (resid 37...
31(chain C and (resid 31 through 36 or (resid 37...
41(chain D and (resid 31 through 37 or (resid 38...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 31 through 36 or (resid 37...A31 - 36
121(chain A and (resid 31 through 36 or (resid 37...A37 - 38
131(chain A and (resid 31 through 36 or (resid 37...A30 - 1494
141(chain A and (resid 31 through 36 or (resid 37...A30 - 1494
151(chain A and (resid 31 through 36 or (resid 37...A30 - 1494
161(chain A and (resid 31 through 36 or (resid 37...A30 - 1494
211(chain B and (resid 31 through 36 or (resid 37...B31 - 36
221(chain B and (resid 31 through 36 or (resid 37...B37 - 38
231(chain B and (resid 31 through 36 or (resid 37...B30 - 1494
241(chain B and (resid 31 through 36 or (resid 37...B30 - 1494
251(chain B and (resid 31 through 36 or (resid 37...B30 - 1494
261(chain B and (resid 31 through 36 or (resid 37...B30 - 1494
311(chain C and (resid 31 through 36 or (resid 37...C31 - 36
321(chain C and (resid 31 through 36 or (resid 37...C37 - 38
331(chain C and (resid 31 through 36 or (resid 37...C30 - 1494
341(chain C and (resid 31 through 36 or (resid 37...C30 - 1494
351(chain C and (resid 31 through 36 or (resid 37...C30 - 1494
361(chain C and (resid 31 through 36 or (resid 37...C30 - 1494
411(chain D and (resid 31 through 37 or (resid 38...D31 - 37
421(chain D and (resid 31 through 37 or (resid 38...D38
431(chain D and (resid 31 through 37 or (resid 38...D31 - 1494
441(chain D and (resid 31 through 37 or (resid 38...D31 - 1494
451(chain D and (resid 31 through 37 or (resid 38...D31 - 1494
461(chain D and (resid 31 through 37 or (resid 38...D31 - 1494

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Components

#1: Protein
L-ornithine N(5)-monooxygenase / OMO / L-ornithine N(5)-oxygenase / Siderphore biosynthesis protein A


Mass: 55977.543 Da / Num. of mol.: 4 / Mutation: residues 1-28 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Strain: Af293 / Gene: sidA / Production host: Escherichia coli (E. coli)
References: UniProt: E9QYP0, L-ornithine N5-monooxygenase [NAD(P)H]
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.48 Å3/Da / Density % sol: 50.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Enzyme stock solution: 8-10 mg/mL SidA, 1 mM NADP, and 15 mM L-Orn in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium ...Details: Enzyme stock solution: 8-10 mg/mL SidA, 1 mM NADP, and 15 mM L-Orn in 25 mM HEPES (pH 7.5) and 100 mM NaCl. Crystallization reservoir: 17-21 % PEG-3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate. Cryo-buffer: 15 % PEG-200, 20 % PEG 3350, 0.1 M HEPES (pH 7.5), 0.1 M calcium acetate, 100 mM NADPH and 15 mM L-Orn

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.335→153.01 Å / Num. obs: 90888 / % possible obs: 98.5 % / Redundancy: 4.1 % / CC1/2: 0.984 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.111 / Rrim(I) all: 0.227 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.34-2.382.91.372955932920.3520.8741.6370.871.9
12.79-153.0140.02523695900.9990.0140.02941.998.9

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Processing

Software
NameVersionClassification
Aimless0.5.23data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B63

4b63


Resolution: 2.335→56.899 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 4400 4.85 %
Rwork0.1835 86295 -
obs0.1866 90695 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.01 Å2 / Biso mean: 34.6665 Å2 / Biso min: 10.46 Å2
Refinement stepCycle: final / Resolution: 2.335→56.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13964 0 387 398 14749
Biso mean--28.98 29.88 -
Num. residues----1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714751
X-RAY DIFFRACTIONf_angle_d1.0220107
X-RAY DIFFRACTIONf_dihedral_angle_d16.0628915
X-RAY DIFFRACTIONf_chiral_restr0.0572250
X-RAY DIFFRACTIONf_plane_restr0.0072584
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8378X-RAY DIFFRACTION8.348TORSIONAL
12B8378X-RAY DIFFRACTION8.348TORSIONAL
13C8378X-RAY DIFFRACTION8.348TORSIONAL
14D8378X-RAY DIFFRACTION8.348TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3352-2.36180.3375780.2987160855
2.3618-2.38960.34381470.2893288799
2.3896-2.41870.33141560.26782930100
2.4187-2.44930.32521750.26312857100
2.4493-2.48160.33641540.26212904100
2.4816-2.51550.32181670.25732899100
2.5155-2.55150.31521590.24482913100
2.5515-2.58960.3121620.23912905100
2.5896-2.630.32241730.23642880100
2.63-2.67320.34731460.23732920100
2.6732-2.71920.32881470.22962889100
2.7192-2.76870.26711490.22262964100
2.7687-2.82190.29471670.21072876100
2.8219-2.87950.29471630.20672896100
2.8795-2.94220.27741370.21532984100
2.9422-3.01060.29091550.20952910100
3.0106-3.08590.29011510.19372869100
3.0859-3.16930.2461630.19642919100
3.1693-3.26260.25731490.18872935100
3.2626-3.36780.26121420.18222943100
3.3678-3.48820.2371430.17932906100
3.4882-3.62780.24481260.16882939100
3.6278-3.79290.24111410.16482925100
3.7929-3.99280.24351290.15722952100
3.9928-4.24290.16991370.14242926100
4.2429-4.57040.19371430.1318295699
4.5704-5.03010.16781310.1287292799
5.0301-5.75730.1851310.14532927100
5.7573-7.25130.20881560.15912958100
7.2513-56.8990.17021230.1509299199
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)
10.3834-0.1148-0.0070.497-0.09570.78750.0038-0.11790.03030.07330.017-0.11040.00940.0631-0.01450.21640.0065-0.0310.2925-0.03160.2539120.67660.901754.6436
20.59640.0988-0.19170.6014-0.09360.3336-0.01180.0099-0.1329-0.0015-0.01950.00780.0763-0.05220.03260.2195-0.0166-0.01870.24250.00470.25784.2214-21.393833.895
30.3655-0.12880.14280.9467-0.31631.1333-0.00870.01350.03720.04850.01260.0631-0.1658-0.0876-0.01020.18540.01720.01070.21870.00750.224985.165723.268423.6452
40.54810.1977-0.0890.4428-0.36380.9402-0.04960.1315-0.0265-0.1099-0.0056-0.12070.16740.10120.06510.23140.03050.0220.3026-0.02760.2331123.99620.89188.7369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A'A0
2X-RAY DIFFRACTION2chain 'B'B0
3X-RAY DIFFRACTION3chain 'C'C0
4X-RAY DIFFRACTION4chain 'D'D0

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