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- PDB-3s5w: Ornithine Hydroxylase (PvdA) from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 3s5w
TitleOrnithine Hydroxylase (PvdA) from Pseudomonas aeruginosa
ComponentsL-ornithine 5-monooxygenase
KeywordsOXIDOREDUCTASE / CLASS B FLAVIN DEPENDENT N-HYDROXYLATING MONOOXYGENASE / Class B Flavin Dependent Monooxygenase N-Hydroxylating / Monooxygenase / 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / N~5~-hydroxy-L-ornithine / PHOSPHATE ION / L-ornithine N(5)-monooxygenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)107,06111
Polymers103,4222
Non-polymers3,6399
Water6,774376
1
A: L-ornithine 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5786
Polymers51,7111
Non-polymers1,8675
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: L-ornithine 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4835
Polymers51,7111
Non-polymers1,7724
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.943, 130.943, 318.521
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

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 385 molecules

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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ONH / N~5~-hydroxy-L-ornithine


Type: L-peptide linking / Mass: 148.160 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O3
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 3.3 Å3/Da / Density % sol: 62.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 9.5% PEG 8000, 25% glycerol, 60 mM potassium phosphate monobasic, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2009
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→36.8 Å / Num. all: 111425 / Num. obs: 108180 / % possible obs: 99.7 %
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 4.1 / % possible all: 97.5

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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: 2.8 A Seleno-SAD PVDA MODEL

Resolution: 1.9→36.74 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.441 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R Free: 0.111
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21735 5403 5 %RANDOM
Rwork0.1918 ---
obs0.19311 102726 99.36 %-
all-103383 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.838 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6547 0 211 376 7134
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0216916
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9939400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.71323.097339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211565
X-RAY DIFFRACTIONr_chiral_restr0.1030.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215251
X-RAY DIFFRACTIONr_mcbond_it0.9481.54107
X-RAY DIFFRACTIONr_mcangle_it1.78826597
X-RAY DIFFRACTIONr_scbond_it2.72632809
X-RAY DIFFRACTIONr_scangle_it4.3074.52801
LS refinement shellResolution: 1.9→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 369 -
Rwork0.235 7207 -
obs--95.74 %

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