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- PDB-6x0i: Structure of oxidized SidA ornithine hydroxylase with the FAD "in... -

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Basic information

Entry
Database: PDB / ID: 6x0i
TitleStructure of oxidized SidA ornithine hydroxylase with the FAD "in" and complexed with NADP
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 / ergosterol biosynthetic process / cellular response to iron ion starvation / siderophore-iron import into cell / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / secondary metabolite biosynthetic process / NADP+ binding ...L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / ergosterol biosynthetic process / cellular response to iron ion starvation / siderophore-iron import into cell / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / secondary metabolite biosynthetic process / NADP+ binding / 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)234,35120
Polymers227,8394
Non-polymers6,51216
Water19,2581069
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25510 Å2
ΔGint-173 kcal/mol
Surface area68820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.507, 154.868, 90.483
Angle α, β, γ (deg.)90.000, 109.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 56959.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: sidA, Afu2g07680 / Production host: Escherichia coli (E. coli)
References: UniProt: E9QYP0, L-ornithine N5-monooxygenase [NAD(P)H]

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Non-polymers , 5 types, 1085 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: 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
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1069 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Enzyme stock solution: 8-10 mg/mL SidA and 1 mM NADP 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- ...Details: Enzyme stock solution: 8-10 mg/mL SidA and 1 mM NADP 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00004 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 1.95→63.21 Å / Num. obs: 151085 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.056 / Rrim(I) all: 0.108 / Net I/σ(I): 12.1 / Num. measured all: 544409 / Scaling rejects: 2
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
1.95-1.983.30.792448774580.5230.5160.9471.599
10.68-63.213.60.02234409540.9990.0140.02646.498.2

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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: 1.95→63.21 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 7476 4.95 %
Rwork0.1682 143516 -
obs0.1703 150992 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.9 Å2 / Biso mean: 30.1353 Å2 / Biso min: 6.28 Å2
Refinement stepCycle: final / Resolution: 1.95→63.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13955 0 477 1069 15501
Biso mean--26.22 31.27 -
Num. residues----1771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00614866
X-RAY DIFFRACTIONf_angle_d0.86920246
X-RAY DIFFRACTIONf_dihedral_angle_d15.5279113
X-RAY DIFFRACTIONf_chiral_restr0.0512234
X-RAY DIFFRACTIONf_plane_restr0.0052581
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.97220.2992400.2588477299
1.9722-1.99540.28182510.2429473599
1.9954-2.01970.27632670.2298473899
2.0197-2.04530.25542640.2192471999
2.0453-2.07220.25072550.2078476299
2.0722-2.10060.24832490.2045472899
2.1006-2.13060.26852460.2004476599
2.1306-2.16240.272460.204478599
2.1624-2.19620.24882170.2013477599
2.1962-2.23220.22162360.1914479499
2.2322-2.27070.22682450.1836477599
2.2707-2.3120.24122610.1918478599
2.312-2.35640.24062670.19164755100
2.3564-2.40450.22432420.18534758100
2.4045-2.45680.22132700.17464793100
2.4568-2.5140.23262810.16974755100
2.514-2.57680.22632240.16414781100
2.5768-2.64650.2062530.1715477599
2.6465-2.72440.21692620.16434770100
2.7244-2.81230.22962590.16974782100
2.8123-2.91290.23572370.17284830100
2.9129-3.02950.23052560.17814791100
3.0295-3.16730.21511980.17354840100
3.1673-3.33430.21722750.17324797100
3.3343-3.54320.20882410.16694804100
3.5432-3.81680.18892340.14914831100
3.8168-4.20080.17382360.13544805100
4.2008-4.80850.13592400.11584829100
4.8085-6.05740.17822700.13484818100
6.0574-63.210.17232540.1592486999
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)
10.71960.1852-0.00350.7889-0.13030.55010.0746-0.1148-0.05770.091-0.045-0.1319-0.02380.1565-0.02620.14480.0006-0.03770.1782-0.03570.1425117.43180.654352.0659
20.78460.3529-0.25510.6544-0.19060.6404-0.0370.1364-0.1431-0.05970.05290.03680.0427-0.1008-0.01550.13240.0043-0.02780.1202-0.0420.182979.7432-21.001332.5775
30.6677-0.0528-0.1371.0215-0.40870.81280.05970.15380.15640.10190.07510.2068-0.2415-0.2249-0.06860.19180.0950.03220.19660.05210.22581.208723.89923.8244
40.755-0.0132-0.21150.8658-0.41120.8423-0.00810.2165-0.0272-0.1468-0.0314-0.19280.14840.12560.03550.19360.05310.01580.2891-0.06740.1729118.6730.36.2768
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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