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- PDB-6x0h: Structure of oxidized SidA ornithine hydroxylase with the FAD in ... -

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Basic information

Entry
Database: PDB / ID: 6x0h
TitleStructure of oxidized 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 / siderophore-dependent iron import into cell / ergosterol biosynthetic process / cellular response to iron ion starvation / 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 / siderophore-dependent iron import into cell / ergosterol biosynthetic process / cellular response to iron ion starvation / siderophore biosynthetic process / N,N-dimethylaniline monooxygenase activity / secondary metabolite biosynthetic process / NADP+ binding / cellular iron ion homeostasis / monooxygenase activity / 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 speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.087 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

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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)227,51915
Polymers223,9104
Non-polymers3,60911
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19810 Å2
ΔGint-137 kcal/mol
Surface area70290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.765, 156.937, 88.651
Angle α, β, γ (deg.)90.000, 110.380, 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 66 or (resid 67...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 31 through 37 or (resid 38...A31 - 37
121(chain A and (resid 31 through 37 or (resid 38...A38
131(chain A and (resid 31 through 37 or (resid 38...A30 - 1492
141(chain A and (resid 31 through 37 or (resid 38...A30 - 1492
151(chain A and (resid 31 through 37 or (resid 38...A30 - 1492
161(chain A and (resid 31 through 37 or (resid 38...A30 - 1492
211(chain B and (resid 31 through 37 or (resid 38...B31 - 37
221(chain B and (resid 31 through 37 or (resid 38...B38
231(chain B and (resid 31 through 37 or (resid 38...B31 - 1492
241(chain B and (resid 31 through 37 or (resid 38...B31 - 1492
251(chain B and (resid 31 through 37 or (resid 38...B31 - 1492
261(chain B and (resid 31 through 37 or (resid 38...B31 - 1492
311(chain C and (resid 31 through 37 or (resid 38...C31 - 37
321(chain C and (resid 31 through 37 or (resid 38...C38
331(chain C and (resid 31 through 37 or (resid 38...C31 - 1492
341(chain C and (resid 31 through 37 or (resid 38...C31 - 1492
351(chain C and (resid 31 through 37 or (resid 38...C31 - 1492
361(chain C and (resid 31 through 37 or (resid 38...C31 - 1492
411(chain D and (resid 31 through 66 or (resid 67...D31 - 66
421(chain D and (resid 31 through 66 or (resid 67...D67 - 75
431(chain D and (resid 31 through 66 or (resid 67...D31 - 1492
441(chain D and (resid 31 through 66 or (resid 67...D31 - 1492
451(chain D and (resid 31 through 66 or (resid 67...D31 - 1492
461(chain D and (resid 31 through 66 or (resid 67...D31 - 1492

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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 / 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]

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Non-polymers , 5 types, 537 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#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 / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.24 Å3/Da / Density % sol: 44.98 %
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

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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: 2.087→156.94 Å / Num. obs: 114542 / % possible obs: 98.4 % / Redundancy: 2.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.088 / Rrim(I) all: 0.142 / Net I/σ(I): 6
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
2.09-2.122.20.8581092650540.4160.7021.113187.4
11.43-156.942.40.02516596960.9970.020.03217.695.4

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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
Resolution: 2.087→65.411 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 5716 4.99 %
Rwork0.1823 108770 -
obs0.1849 114486 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.4 Å2 / Biso mean: 37.5202 Å2 / Biso min: 11.92 Å2
Refinement stepCycle: final / Resolution: 2.087→65.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13867 0 240 526 14633
Biso mean--33.89 33.85 -
Num. residues----1788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714423
X-RAY DIFFRACTIONf_angle_d0.91919611
X-RAY DIFFRACTIONf_dihedral_angle_d14.9038824
X-RAY DIFFRACTIONf_chiral_restr0.0552192
X-RAY DIFFRACTIONf_plane_restr0.0062538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A8096X-RAY DIFFRACTION9.086TORSIONAL
12B8096X-RAY DIFFRACTION9.086TORSIONAL
13C8096X-RAY DIFFRACTION9.086TORSIONAL
14D8096X-RAY DIFFRACTION9.086TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.087-2.11050.33211640.2856301682
2.1105-2.13530.36581780.28364199
2.1353-2.16140.28961760.2705364799
2.1614-2.18870.33571990.2649362599
2.1887-2.21750.28151650.2578368799
2.2175-2.24790.31471780.2515363799
2.2479-2.280.30451860.2407364199
2.28-2.31410.29941890.2364367499
2.3141-2.35020.29982160.2251360699
2.3502-2.38870.29582020.2245366499
2.3887-2.42990.29422050.2205364099
2.4299-2.47410.26821810.20653680100
2.4741-2.52170.24841970.2029363399
2.5217-2.57320.28651880.20063708100
2.5732-2.62910.25531740.19563664100
2.6291-2.69030.24161870.1934367999
2.6903-2.75760.23891900.1843648100
2.7576-2.83210.23972020.1843658100
2.8321-2.91550.24731940.19093671100
2.9155-3.00960.25781890.19583691100
3.0096-3.11710.2632330.2023608100
3.1171-3.24190.25632120.19333660100
3.2419-3.38950.24262070.1781365799
3.3895-3.56820.18821860.1702364499
3.5682-3.79170.20611860.1565364598
3.7917-4.08440.18831840.1449361998
4.0844-4.49540.16981780.1304364797
4.4954-5.14560.17711920.1313358697
5.1456-6.48210.20931770.1604360997
6.4821-65.4110.16962010.1573358596
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.57780.09890.11970.7993-0.08310.46580.0069-0.0206-0.01410.03590.0022-0.1226-0.04750.1019-0.00320.1985-0.0164-0.00260.2075-0.02190.2297112.16030.436550.0706
20.56410.2391-0.13490.7605-0.16540.62440.01120.0964-0.0357-0.0973-0.00920.0690.0236-0.0618-0.00930.2040.013-0.02270.1988-0.02460.265574.7609-21.671231.4295
30.6214-0.01930.14570.7959-0.42960.8677-0.08630.11710.086-0.0040.0930.1123-0.1211-0.0748-0.00790.2307-0.0133-0.01060.23090.00860.258575.926123.486321.9164
41.27940.39530.15660.576-0.20260.6903-0.15750.593-0.1041-0.14670.1573-0.17880.09130.23680.02410.2766-0.05840.05490.5689-0.09710.2466112.56640.71444.5046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A')A0
2X-RAY DIFFRACTION2(chain 'B')B0
3X-RAY DIFFRACTION3(chain 'C')C0
4X-RAY DIFFRACTION4(chain 'D')D0

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