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- PDB-4b65: A. fumigatus ornithine hydroxylase (SidA), reduced state bound to... -

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Basic information

Entry
Database: PDB / ID: 4b65
TitleA. fumigatus ornithine hydroxylase (SidA), reduced state bound to NADP(H)
ComponentsL-ORNITHINE N5 MONOOXYGENASE
KeywordsOXIDOREDUCTASE / SIDEROPHORE / FLAVIN
Function / homology
Function and homology information


L-ornithine N5-monooxygenase [NAD(P)H] / ferrichrome biosynthetic process / ornithine N5-monooxygenase activity / ergosterol biosynthetic process / cellular response to iron ion starvation / siderophore-iron import into cell / 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 / ergosterol biosynthetic process / cellular response to iron ion starvation / siderophore-iron import into cell / 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 / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-NDP / L-ornithine N(5)-monooxygenase / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesASPERGILLUS FUMIGATUS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsFranceschini, S. / Fedkenheuer, M. / Vogelaar, N.J. / Robinson, H.H. / Sobrado, P. / Mattevi, A.
CitationJournal: Biochemistry / Year: 2012
Title: Structural Insight Into the Mechanism of Oxygen Activation and Substrate Selectivity of Flavin-Dependent N-Hydroxylating Monooxygenases.
Authors: Franceschini, S. / Fedkenheuer, M. / Vogelaar, N.J. / Robinson, H.H. / Sobrado, P. / Mattevi, A.
History
DepositionAug 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ORNITHINE N5 MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9558
Polymers56,9601
Non-polymers1,9957
Water3,495194
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)235,82032
Polymers227,8394
Non-polymers7,98228
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area29420 Å2
ΔGint-218.2 kcal/mol
Surface area71960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.990, 84.460, 145.620
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-2045-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein L-ORNITHINE N5 MONOOXYGENASE / L-ORNITHINE N5-OXYGENASE


Mass: 56959.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ASPERGILLUS FUMIGATUS (mold) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SE95, UniProt: E9QYP0*PLUS

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Non-polymers , 5 types, 201 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.11 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.6
Details: HANGING DROP VAPOR DIFFUSION METHOD, WITH A RESERVOIR SOLUTION CONTAINING; 1.6 M AMMONIUM SULFATE, 0.1 M HEPES, 2% DIOXANE, PH 6.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 21091 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.8
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B63

4b63


Resolution: 2.32→72.81 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 10.261 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.447 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.25013 1074 5.1 %RANDOM
Rwork0.19593 ---
obs0.19877 20014 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.449 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.32→72.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 130 194 3896
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193843
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9955235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87823.295173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34215636
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3741533
X-RAY DIFFRACTIONr_chiral_restr0.0720.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212891
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 66 -
Rwork0.232 1325 -
obs--97.14 %
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)
12.77340.07641.40251.00150.10261.057-0.0329-0.04930.06190.09750.014-0.0483-0.03860.09250.01880.0142-0.00840.0180.0571-0.0170.2924-20.255-30.33930.515
21.30830.53240.79451.17360.40192.4312-0.05920.06410.17750.05390.0122-0.0235-0.36450.12040.0470.0724-0.01520.0330.01760.01670.337-20.725-19.151-2.725
30.44150.41991.55840.40821.43455.76260.01540.129-0.00050.00640.08050.00430.22870.5942-0.09590.07890.06460.0040.1320.01070.4125-14.787-44.55414.462
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 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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