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- PDB-4nzh: A. fumigatus flavin-dependent ornithine monooxygenase R279A mutant -

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Basic information

Entry
Database: PDB / ID: 4nzh
TitleA. fumigatus flavin-dependent ornithine monooxygenase R279A mutant
ComponentsL-ornithine N5 monooxygenase
KeywordsOXIDOREDUCTASE
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 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain superfamily / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-ornithine N(5)-monooxygenase / FLAVIN-ADENINE DINUCLEOTIDE / L-ornithine / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRobinson, R. / Franceschini, S. / Sobrado, P.
CitationJournal: To be Published
Title: A. fumigatus flavin-dependent ornithine monooxygenase R279A mutant
Authors: Robinson, R. / Franceschini, S. / Sobrado, P.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ornithine N5 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1607
Polymers56,8741
Non-polymers1,2866
Water3,675204
1
A: L-ornithine N5 monooxygenase
hetero molecules

A: L-ornithine N5 monooxygenase
hetero molecules

A: L-ornithine N5 monooxygenase
hetero molecules

A: L-ornithine N5 monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,63928
Polymers227,4944
Non-polymers5,14424
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 area21720 Å2
ΔGint-119 kcal/mol
Surface area71890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.905, 84.083, 144.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-803-

HOH

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Components

#1: Protein L-ornithine N5 monooxygenase / / L-ornithine N5-oxygenase


Mass: 56873.562 Da / Num. of mol.: 1 / Mutation: R279A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: sidA / Plasmid: pET15a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SE95, UniProt: E9QYP0*PLUS
#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-ORN / L-ornithine / Ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.08 Å3/Da / Density % sol: 40.95 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 6.6
Details: 1.6 M ammonium sulfate, 0.1 M HEPES, 2% dioxane, pH 6.6, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 32887 / Num. obs: 32825 / % possible obs: 99 % / Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0119refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.964 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24262 1681 5.2 %RANDOM
Rwork0.2062 ---
obs0.20812 30804 98.53 %-
all-32887 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0 Å2
2---0.01 Å2-0 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2→27.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 86 204 3778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193690
X-RAY DIFFRACTIONr_angle_refined_deg0.9641.9815015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8185457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97723.515165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215606
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7661529
X-RAY DIFFRACTIONr_chiral_restr0.0640.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212795
X-RAY DIFFRACTIONr_mcbond_it0.5031.6141807
X-RAY DIFFRACTIONr_mcangle_it0.9132.4092255
X-RAY DIFFRACTIONr_scbond_it0.4761.711880
X-RAY DIFFRACTIONr_long_range_B_refined6.20514.395657
LS refinement shellResolution: 1.992→2.043 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 119 -
Rwork0.267 2126 -
obs--93 %
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)
13.88180.45671.82670.89320.36961.1893-0.0358-0.0760.1410.07750.0119-0.0779-0.06350.04060.02380.1668-0.00630.01730.0198-0.01440.2305-20.255-30.33930.515
21.60860.76661.43071.67030.75743.1151-0.00620.07740.09260.0831-0.0148-0.1975-0.28130.18830.0210.2774-0.02550.03260.01440.02020.2961-20.725-19.151-2.725
33.16472.42283.97471.86723.04094.9943-0.08340.3761-0.0233-0.04830.1966-0.0244-0.03650.4824-0.11320.28810.03480.0840.1674-0.05070.4713-14.787-44.55414.462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 213
2X-RAY DIFFRACTION1A408 - 455
3X-RAY DIFFRACTION1A464 - 489
4X-RAY DIFFRACTION2A214 - 284
5X-RAY DIFFRACTION2A324 - 407
6X-RAY DIFFRACTION3A287 - 323
7X-RAY DIFFRACTION3A457 - 463

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