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- PDB-3s61: Reduced Form of Ornithine Hydroxylase (PvdA) from Pseudomonas aer... -

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Basic information

Entry
Database: PDB / ID: 3s61
TitleReduced Form of Ornithine Hydroxylase (PvdA) from Pseudomonas aeruginosa
ComponentsL-ornithine 5-monooxygenase
KeywordsOXIDOREDUCTASE / N5-L-Ornithine monooxygenase / reduced form / class B flavin dependent N-hydroxylating monooxygenase / ornithine hydroxylase / bacterial cytosol
Function / homology
Function and homology information


L-ornithine N5-monooxygenase (NADPH) / ornithine N5-monooxygenase activity / pyoverdine biosynthetic process / intracellular iron ion homeostasis / plasma membrane / cytoplasm
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 / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsOlucha, J. / Lamb, A.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Two Structures of an N-Hydroxylating Flavoprotein Monooxygenase: ORNITHINE HYDROXYLASE FROM PSEUDOMONAS AERUGINOSA.
Authors: Olucha, J. / Meneely, K.M. / Chilton, A.S. / Lamb, A.L.
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2011Group: Database references
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ornithine 5-monooxygenase
B: L-ornithine 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7498
Polymers103,4222
Non-polymers3,3266
Water0
1
A: L-ornithine 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3744
Polymers51,7111
Non-polymers1,6633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-ornithine 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3744
Polymers51,7111
Non-polymers1,6633
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.162, 128.162, 316.514
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsAUTHORS STATE THAT DYNAMIC LIGHT SCATTERING EXPERIMENTS HAVE SHOWN PVDA BEHAVES AS A MONOMER IN SOLUTION (MENEELY, K.M. AND LAMB, A.L., BIOCHEMISTRY, 2007, 46 (42), 11930-11937).

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Components

#1: Protein L-ornithine 5-monooxygenase / L-ornithine N(5)-oxygenase


Mass: 51711.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2386, pvd-1, pvdA / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q51548, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or ...References: UniProt: Q51548, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of one atom of oxygen (internal monooxygenases or internal mixed-function oxidases)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3

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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: 3.14 Å3/Da / Density % sol: 60.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 9.5% PEG 8000, 25% glycerol, 60 mM potassium phosphate monobasic, Reducing agent Sodium Dithionite, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 18, 2011
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.03→39.26 Å / Num. all: 27042 / Num. obs: 26002 / % possible obs: 96 %
Reflection shellResolution: 3.03→3.19 Å / Mean I/σ(I) obs: 5.8 / % possible all: 96

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0110refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Oxidized form of PvdA

Resolution: 3.03→39.26 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.886 / SU B: 18.131 / SU ML: 0.332 / Cross valid method: THROUGHOUT / ESU R Free: 0.46
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27183 2616 10.1 %RANDOM
Rwork0.21571 ---
obs0.22139 23360 99.47 %-
all-23484 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.172 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.03→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 220 0 6760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216910
X-RAY DIFFRACTIONr_angle_refined_deg1.8191.9949389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8055817
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1523.136338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.538151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.931564
X-RAY DIFFRACTIONr_chiral_restr0.1070.21026
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215246
X-RAY DIFFRACTIONr_mcbond_it0.6811.54095
X-RAY DIFFRACTIONr_mcangle_it1.326572
X-RAY DIFFRACTIONr_scbond_it1.56532815
X-RAY DIFFRACTIONr_scangle_it2.6434.52817
LS refinement shellResolution: 3.03→3.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 176 -
Rwork0.257 1569 -
obs--92.72 %

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