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- PDB-7jvk: Structure of the M101A variant of the SidA ornithine hydroxylase ... -

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Basic information

Entry
Database: PDB / ID: 7jvk
TitleStructure of the M101A variant of the SidA ornithine hydroxylase with the FAD in the "out" conformation
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 / cellular response to iron ion starvation / siderophore-iron import into cell / ergosterol biosynthetic process / 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 / cellular response to iron ion starvation / siderophore-iron import into cell / ergosterol biosynthetic process / 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 / TRIETHYLENE GLYCOL / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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: Biochemistry / Year: 2020
Title: Structural Determinants of Flavin Dynamics in a Class B Monooxygenase.
Authors: Campbell, A.C. / Robinson, R. / Mena-Aguilar, D. / Sobrado, P. / Tanner, J.J.
History
DepositionAug 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,35716
Polymers227,5984
Non-polymers3,75912
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20240 Å2
ΔGint-133 kcal/mol
Surface area69760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.437, 155.275, 88.271
Angle α, β, γ (deg.)90.000, 110.330, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 31 through 37 or (resid 38...
21(chain B and (resid 31 through 37 or (resid 38...
31(chain C and (resid 31 through 37 or (resid 38...
41(chain D and (resid 31 through 37 or (resid 38...

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
11LEULEUASPASP(chain A and (resid 31 through 37 or (resid 38...AA31 - 3731 - 37
12GLUGLUGLUGLU(chain A and (resid 31 through 37 or (resid 38...AA3838
13ARGARGARGARG(chain A and (resid 31 through 37 or (resid 38...AA30 - 48930 - 489
14ARGARGARGARG(chain A and (resid 31 through 37 or (resid 38...AA30 - 48930 - 489
15ARGARGARGARG(chain A and (resid 31 through 37 or (resid 38...AA30 - 48930 - 489
16ARGARGARGARG(chain A and (resid 31 through 37 or (resid 38...AA30 - 48930 - 489
21LEULEUASPASP(chain B and (resid 31 through 37 or (resid 38...BB31 - 3731 - 37
22GLUGLUGLUGLU(chain B and (resid 31 through 37 or (resid 38...BB3838
23LEULEUHOHHOH(chain B and (resid 31 through 37 or (resid 38...BB - R31 - 70131
24LEULEUHOHHOH(chain B and (resid 31 through 37 or (resid 38...BB - R31 - 70131
25LEULEUHOHHOH(chain B and (resid 31 through 37 or (resid 38...BB - R31 - 70131
26LEULEUHOHHOH(chain B and (resid 31 through 37 or (resid 38...BB - R31 - 70131
31LEULEUASPASP(chain C and (resid 31 through 37 or (resid 38...CC31 - 3731 - 37
32GLUGLUGLUGLU(chain C and (resid 31 through 37 or (resid 38...CC3838
33ARGARGARGARG(chain C and (resid 31 through 37 or (resid 38...CC30 - 48930 - 489
34ARGARGARGARG(chain C and (resid 31 through 37 or (resid 38...CC30 - 48930 - 489
35ARGARGARGARG(chain C and (resid 31 through 37 or (resid 38...CC30 - 48930 - 489
36ARGARGARGARG(chain C and (resid 31 through 37 or (resid 38...CC30 - 48930 - 489
41LEULEUASPASP(chain D and (resid 31 through 37 or (resid 38...DD31 - 3731 - 37
42GLUGLUGLUGLU(chain D and (resid 31 through 37 or (resid 38...DD3838
43ARGARGGLUGLU(chain D and (resid 31 through 37 or (resid 38...DD30 - 48830 - 488
44ARGARGGLUGLU(chain D and (resid 31 through 37 or (resid 38...DD30 - 48830 - 488
45ARGARGGLUGLU(chain D and (resid 31 through 37 or (resid 38...DD30 - 48830 - 488
46ARGARGGLUGLU(chain D and (resid 31 through 37 or (resid 38...DD30 - 48830 - 488

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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: 56899.562 Da / Num. of mol.: 4 / Mutation: M101A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (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, 399 molecules

#2: 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
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Enzyme stock solution: 8-10 mg/ml SidA (M101A) 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: ...Details: Enzyme stock solution: 8-10 mg/ml SidA (M101A) 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. Drop ratio: 2 enzyme to 1 reservoir

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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 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→61.44 Å / Num. obs: 96363 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.995 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.067 / Rrim(I) all: 0.128 / Net I/σ(I): 10.8 / Num. measured all: 340416 / Scaling rejects: 173
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
2.2-2.242.81.2351223043150.4840.8591.5140.989.2
12.05-61.443.60.02421676100.990.0160.02944.397.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6X0H

6x0h


Resolution: 2.2→56.63 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 1927 2 %
Rwork0.1945 94342 -
obs0.1952 96269 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.23 Å2 / Biso mean: 34.8222 Å2 / Biso min: 16.32 Å2
Refinement stepCycle: final / Resolution: 2.2→56.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13919 0 250 387 14556
Biso mean--28.87 30.05 -
Num. residues----1797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714485
X-RAY DIFFRACTIONf_angle_d0.94219694
X-RAY DIFFRACTIONf_dihedral_angle_d20.2035444
X-RAY DIFFRACTIONf_chiral_restr0.0542204
X-RAY DIFFRACTIONf_plane_restr0.0062547
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6207X-RAY DIFFRACTION9.134TORSIONAL
12B6207X-RAY DIFFRACTION9.134TORSIONAL
13C6207X-RAY DIFFRACTION9.134TORSIONAL
14D6207X-RAY DIFFRACTION9.134TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.37821170.33416047616488
2.26-2.320.27661440.27186588673297
2.32-2.380.31131470.242967756922100
2.38-2.460.29351490.231668046953100
2.46-2.550.29391500.228868026952100
2.55-2.650.31681420.22467716913100
2.65-2.770.23691530.22167926945100
2.77-2.920.27971190.218568316950100
2.92-3.10.29231270.22467886915100
3.1-3.340.25811210.202868626983100
3.34-3.680.18011230.18636803692699
3.68-4.210.20421240.16066774689899
4.21-5.30.17031560.138968146970100
5.3-56.630.17231550.1586891704699
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)
10.5837-0.01120.14150.9153-0.08630.49380.0232-0.0477-0.00820.03340.0129-0.123-0.03470.103-0.02950.2158-0.0128-0.01890.223-0.03340.2259111.75060.582149.9187
20.58950.2446-0.19060.5573-0.02690.65930.00370.052-0.0372-0.0638-0.00320.05550.0049-0.0584-0.00240.18140.0102-0.02360.1462-0.01820.219174.4743-21.410431.4727
30.68750.040.05680.7743-0.31210.9043-0.05960.07180.06280.02050.06620.1121-0.069-0.0789-0.00770.2709-0.00610.00240.21760.00020.266775.708423.427921.7235
40.78360.2331-0.05760.6648-0.1870.6735-0.08250.3152-0.1135-0.16550.0737-0.16550.07170.19230.01410.2766-0.02320.03810.4184-0.08070.2345112.53930.98744.0274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 501
2X-RAY DIFFRACTION2chain BB1 - 501
3X-RAY DIFFRACTION3chain CC1 - 501
4X-RAY DIFFRACTION4chain DD1 - 501

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