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- PDB-5cku: Structure of Aspergillus fumigatus ornithine hydroxylase (SidA) m... -

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Basic information

Entry
Database: PDB / ID: 5cku
TitleStructure of Aspergillus fumigatus ornithine hydroxylase (SidA) mutant N323A bound to NADP and ornithine
ComponentsL-ornithine N(5)-monooxygenase
KeywordsOXIDOREDUCTASE / SIDEROPHORE / FLAVIN
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 / N,N-dimethylaniline monooxygenase activity / siderophore biosynthetic process / 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 / N,N-dimethylaniline monooxygenase activity / siderophore biosynthetic process / 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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-ornithine / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsTanner, J.J. / Qureshi, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1021384 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2015
Title: Contribution to catalysis of ornithine binding residues in ornithine N5-monooxygenase.
Authors: Robinson, R. / Qureshi, I.A. / Klancher, C.A. / Rodriguez, P.J. / Tanner, J.J. / Sobrado, P.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,9588
Polymers56,9171
Non-polymers2,0417
Water3,243180
1
A: L-ornithine N(5)-monooxygenase
hetero molecules

A: L-ornithine N(5)-monooxygenase
hetero molecules

A: L-ornithine N(5)-monooxygenase
hetero molecules

A: L-ornithine N(5)-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,83232
Polymers227,6674
Non-polymers8,16628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area25490 Å2
ΔGint-300 kcal/mol
Surface area69050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.081, 84.002, 145.057
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 56916.656 Da / Num. of mol.: 1 / Mutation: N323A
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 , 6 types, 187 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: 2.06 Å3/Da / Density % sol: 40.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.1 M HEPES, pH 6.6, 1.86 M ammonium sulfate, and 1% (v/v) dioxane. Protein stock solution contained 8 mg/mL enzyme with 1 mM NADP+ and 100 mM L-ornithine.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→72.69 Å / Num. obs: 27670 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 23.14 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.058 / Net I/σ(I): 9.3 / Num. measured all: 156743 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.1-2.165.60.6172.71237722280.8610.28100
8.91-72.695.50.0522.620953830.9970.02294.4

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4B63

4b63


Resolution: 2.1→72.69 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 1420 5.13 %
Rwork0.1724 26247 -
obs0.1752 27667 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.19 Å2 / Biso mean: 28.2947 Å2 / Biso min: 11.7 Å2
Refinement stepCycle: final / Resolution: 2.1→72.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3472 0 114 180 3766
Biso mean--35.83 27.81 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073670
X-RAY DIFFRACTIONf_angle_d1.0365003
X-RAY DIFFRACTIONf_chiral_restr0.04556
X-RAY DIFFRACTIONf_plane_restr0.005635
X-RAY DIFFRACTIONf_dihedral_angle_d16.1671334
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.17510.2821420.221225632705100
2.1751-2.26220.24631270.196526172744100
2.2622-2.36510.27741420.193826232765100
2.3651-2.48980.28361620.193526022764100
2.4898-2.64580.27231620.188426082770100
2.6458-2.85010.2441580.196126032761100
2.8501-3.13690.21071240.191926422766100
3.1369-3.59080.24681160.1722661277799
3.5908-4.5240.18011240.13422671279599
4.524-72.73640.18991630.15032657282096
Refinement TLS params.Method: refined / Origin x: -19.8614 Å / Origin y: -27.6361 Å / Origin z: 18.0043 Å
111213212223313233
T0.142 Å2-0.0197 Å20.0019 Å2-0.1376 Å2-0.0147 Å2--0.2497 Å2
L0.3579 °20.0287 °20.1961 °2-0.2317 °2-0.0216 °2--0.9749 °2
S0.0143 Å °-0.0219 Å °0.0932 Å °0.0098 Å °-0.0218 Å °-0.1034 Å °-0.1162 Å °0.1491 Å °0.0097 Å °
Refinement TLS groupSelection details: (chain A and not resname FAD)

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