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- PDB-6x0k: Structure of dithionite-reduced SidA ornithine hydroxylase with t... -

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Basic information

Entry
Database: PDB / ID: 6x0k
TitleStructure of dithionite-reduced SidA ornithine hydroxylase with the FAD "in" and complexed with 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 / L-ornithine / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.231 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
E: L-ornithine N(5)-monooxygenase
F: L-ornithine N(5)-monooxygenase
G: L-ornithine N(5)-monooxygenase
H: L-ornithine N(5)-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)454,91422
Polymers447,8208
Non-polymers7,09314
Water6,900383
1
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)227,45711
Polymers223,9104
Non-polymers3,5477
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18160 Å2
ΔGint-116 kcal/mol
Surface area70010 Å2
MethodPISA
2
E: L-ornithine N(5)-monooxygenase
F: L-ornithine N(5)-monooxygenase
G: L-ornithine N(5)-monooxygenase
H: L-ornithine N(5)-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,45711
Polymers223,9104
Non-polymers3,5477
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18200 Å2
ΔGint-117 kcal/mol
Surface area69110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.902, 155.044, 146.846
Angle α, β, γ (deg.)90.000, 91.010, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 31 or (resid 32 through 33...
21(chain B and (resid 31 through 32 or (resid 33...
31(chain C and (resid 31 through 35 or (resid 36...
41(chain D and (resid 31 through 32 or (resid 33...
51(chain E and (resid 31 through 32 or (resid 33...
61(chain F and (resid 31 through 32 or (resid 33...
71(chain G and (resid 31 through 35 or (resid 36...
81(chain H and (resid 31 or (resid 32 through 33...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEU(chain A and (resid 31 or (resid 32 through 33...AA3124
12ARGARGSERSER(chain A and (resid 31 or (resid 32 through 33...AA32 - 3325 - 26
13LEULEUGLUGLU(chain A and (resid 31 or (resid 32 through 33...AA31 - 48824 - 481
14LEULEUGLUGLU(chain A and (resid 31 or (resid 32 through 33...AA31 - 48824 - 481
15LEULEUGLUGLU(chain A and (resid 31 or (resid 32 through 33...AA31 - 48824 - 481
16LEULEUGLUGLU(chain A and (resid 31 or (resid 32 through 33...AA31 - 48824 - 481
21LEULEUARGARG(chain B and (resid 31 through 32 or (resid 33...BB31 - 3224 - 25
22SERSERSERSER(chain B and (resid 31 through 32 or (resid 33...BB3326
23LEULEUGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB31 - 48824 - 481
24LEULEUGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB31 - 48824 - 481
25LEULEUGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB31 - 48824 - 481
26LEULEUGLUGLU(chain B and (resid 31 through 32 or (resid 33...BB31 - 48824 - 481
31LEULEUPROPRO(chain C and (resid 31 through 35 or (resid 36...CC31 - 3524 - 28
32GLNGLNASPASP(chain C and (resid 31 through 35 or (resid 36...CC36 - 3729 - 30
33LEULEUGLUGLU(chain C and (resid 31 through 35 or (resid 36...CC31 - 48824 - 481
34LEULEUGLUGLU(chain C and (resid 31 through 35 or (resid 36...CC31 - 48824 - 481
35LEULEUGLUGLU(chain C and (resid 31 through 35 or (resid 36...CC31 - 48824 - 481
36LEULEUGLUGLU(chain C and (resid 31 through 35 or (resid 36...CC31 - 48824 - 481
41LEULEUARGARG(chain D and (resid 31 through 32 or (resid 33...DD31 - 3224 - 25
42SERSERSERSER(chain D and (resid 31 through 32 or (resid 33...DD3326
43LEULEUGLUGLU(chain D and (resid 31 through 32 or (resid 33...DD31 - 48824 - 481
44LEULEUGLUGLU(chain D and (resid 31 through 32 or (resid 33...DD31 - 48824 - 481
45LEULEUGLUGLU(chain D and (resid 31 through 32 or (resid 33...DD31 - 48824 - 481
46LEULEUGLUGLU(chain D and (resid 31 through 32 or (resid 33...DD31 - 48824 - 481
51LEULEUARGARG(chain E and (resid 31 through 32 or (resid 33...EE31 - 3224 - 25
52SERSERSERSER(chain E and (resid 31 through 32 or (resid 33...EE3326
53LEULEUGLUGLU(chain E and (resid 31 through 32 or (resid 33...EE31 - 48824 - 481
54LEULEUGLUGLU(chain E and (resid 31 through 32 or (resid 33...EE31 - 48824 - 481
55LEULEUGLUGLU(chain E and (resid 31 through 32 or (resid 33...EE31 - 48824 - 481
56LEULEUGLUGLU(chain E and (resid 31 through 32 or (resid 33...EE31 - 48824 - 481
61LEULEUARGARG(chain F and (resid 31 through 32 or (resid 33...FF31 - 3224 - 25
62SERSERSERSER(chain F and (resid 31 through 32 or (resid 33...FF3326
63LEULEUGLUGLU(chain F and (resid 31 through 32 or (resid 33...FF31 - 48824 - 481
64LEULEUGLUGLU(chain F and (resid 31 through 32 or (resid 33...FF31 - 48824 - 481
65LEULEUGLUGLU(chain F and (resid 31 through 32 or (resid 33...FF31 - 48824 - 481
66LEULEUGLUGLU(chain F and (resid 31 through 32 or (resid 33...FF31 - 48824 - 481
71LEULEUPROPRO(chain G and (resid 31 through 35 or (resid 36...GG31 - 3524 - 28
72GLNGLNASPASP(chain G and (resid 31 through 35 or (resid 36...GG36 - 3729 - 30
73LEULEUGLUGLU(chain G and (resid 31 through 35 or (resid 36...GG31 - 48824 - 481
74LEULEUGLUGLU(chain G and (resid 31 through 35 or (resid 36...GG31 - 48824 - 481
75LEULEUGLUGLU(chain G and (resid 31 through 35 or (resid 36...GG31 - 48824 - 481
76LEULEUGLUGLU(chain G and (resid 31 through 35 or (resid 36...GG31 - 48824 - 481
81LEULEULEULEU(chain H and (resid 31 or (resid 32 through 33...HH3124
82ARGARGSERSER(chain H and (resid 31 or (resid 32 through 33...HH32 - 3325 - 26
83LEULEUGLUGLU(chain H and (resid 31 or (resid 32 through 33...HH31 - 48824 - 481
84LEULEUGLUGLU(chain H and (resid 31 or (resid 32 through 33...HH31 - 48824 - 481
85LEULEUGLUGLU(chain H and (resid 31 or (resid 32 through 33...HH31 - 48824 - 481
86LEULEUGLUGLU(chain H and (resid 31 or (resid 32 through 33...HH31 - 48824 - 481

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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.: 8 / 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-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H35N9O15P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: Enzyme stock solution: 8-10 mg/mL SidA 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 % ...Details: Enzyme stock solution: 8-10 mg/mL SidA 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, 50 mM L-ornithine, and 100 mM sodium dithionite

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.23→155.04 Å / Num. obs: 225621 / % possible obs: 97.6 % / Redundancy: 4.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.113 / Rrim(I) all: 0.239 / Net I/σ(I): 7.8 / Num. measured all: 1006051
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
2.23-2.264.41.43742885960.3990.7271.583175.2
12.19-155.043.70.056527914230.9920.0330.06527.896.9

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.14refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B63

4b63


Resolution: 2.231→68.553 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 0.31 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 11094 4.98 %
Rwork0.2307 211812 -
obs0.2332 222906 97.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 158.24 Å2 / Biso mean: 57.4771 Å2 / Biso min: 21.41 Å2
Refinement stepCycle: final / Resolution: 2.231→68.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27310 0 425 383 28118
Biso mean--47.06 42.97 -
Num. residues----3511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00828413
X-RAY DIFFRACTIONf_angle_d1.02938612
X-RAY DIFFRACTIONf_dihedral_angle_d14.71817376
X-RAY DIFFRACTIONf_chiral_restr0.0584320
X-RAY DIFFRACTIONf_plane_restr0.0074990
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A15336X-RAY DIFFRACTION8.825TORSIONAL
12B15336X-RAY DIFFRACTION8.825TORSIONAL
13C15336X-RAY DIFFRACTION8.825TORSIONAL
14D15336X-RAY DIFFRACTION8.825TORSIONAL
15E15336X-RAY DIFFRACTION8.825TORSIONAL
16F15336X-RAY DIFFRACTION8.825TORSIONAL
17G15336X-RAY DIFFRACTION8.825TORSIONAL
18H15336X-RAY DIFFRACTION8.825TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2313-2.25670.3582880.3103557576
2.2567-2.28330.33153340.2893678994
2.2833-2.31110.33163320.2897681994
2.3111-2.34040.34263680.3013686195
2.3404-2.37120.35063770.2815695295
2.3712-2.40360.33093630.2722694996
2.4036-2.4380.33533530.2812703597
2.438-2.47440.34683600.2943707097
2.4744-2.5130.37433440.2998680094
2.513-2.55420.34853770.2945714199
2.5542-2.59830.3793560.2946724099
2.5983-2.64550.34953600.2822726599
2.6455-2.69640.33273930.2738715599
2.6964-2.75150.32763960.277716899
2.7515-2.81130.33683490.2751727899
2.8113-2.87670.32944000.2623717399
2.8767-2.94860.33544080.2673717899
2.9486-3.02840.32383950.2807719299
3.0284-3.11750.34053530.29719399
3.1175-3.21810.34273530.2965720199
3.2181-3.33310.32214000.2519717099
3.3331-3.46660.29514330.2409709399
3.4666-3.62430.26344140.2318703897
3.6243-3.81540.27143830.21714998
3.8154-4.05440.24533720.1933719499
4.0544-4.36740.21253650.1708723899
4.3674-4.80680.20943370.1617728299
4.8068-5.50210.21593840.1698720099
5.5021-6.9310.23493430.193723998
6.931-68.5530.23344040.2133717597
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)
11.2199-0.40260.29591.0423-0.41810.9893-0.0436-0.0241-0.30620.1220.11640.22520.0279-0.1675-0.07480.25230.01830.03850.24930.00020.4386-31.0551-50.486372.0344
20.6993-0.0459-0.05321.0078-0.1660.84910.02310.0779-0.0225-0.0750.0504-0.2246-0.08640.3034-0.0620.2426-0.0602-0.00020.4116-0.08870.37298.0696-31.506153.051
30.5965-0.38510.05491.3384-0.19680.6857-0.00960.290.1013-0.37180.08780.1567-0.1325-0.136-0.07970.4073-0.0557-0.0660.46740.08760.3812-28.4674-26.040826.7887
41.3358-0.7120.23751.2831-0.3360.4785-0.1255-0.11810.51890.29360.1205-0.0533-0.2366-0.08020.01880.44570.0816-0.01290.292-0.06960.557-33.9402-5.198468.4601
50.57680.385-0.08511.0177-0.40311.23140.0654-0.1036-0.12680.0310.03330.040.1644-0.2027-0.09910.3068-0.0522-0.02060.3671-0.0140.3846-31.9998-94.280747.6647
60.81990.4454-0.04551.01330.09870.0957-0.08190.4179-0.4357-0.28580.0707-0.15320.2327-0.12510.00750.6598-0.0978-0.0310.6464-0.27280.5981-35.6043-114.25865.2538
71.80.2281-0.35371.1107-0.32991.35930.09590.8480.3476-0.31450.09930.1567-0.1471-0.2861-0.17420.47210.0213-0.01320.69580.10870.3889-28.9971-69.24322.9232
80.84550.5237-0.24711.2133-0.32241.2089-0.02680.2347-0.3310.05360.027-0.43070.09320.49580.00430.41770.0493-0.00430.683-0.18790.62346.9061-91.173824.0241
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
5X-RAY DIFFRACTION5chain 'E'E0
6X-RAY DIFFRACTION6chain 'F'F0
7X-RAY DIFFRACTION7chain 'G'G0
8X-RAY DIFFRACTION8chain 'H'H0

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