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- PDB-5nah: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in compl... -

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Basic information

Entry
Database: PDB / ID: 5nah
TitlePseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with 3-{5-chloro-6-[(1R)-1-(6-methylpyridazin-3-yl)ethoxy]-1,2-benzoxazol-3-yl}propanoic acid
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / KMO
Function / homology
Function and homology information


kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic process / FAD binding
Similarity search - Function
Kynurenine 3-monooxygenase / FAD binding domain / FAD-binding domain / 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
Chem-8RB / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsRowland, P.
CitationJournal: Nat Commun / Year: 2017
Title: Structural and mechanistic basis of differentiated inhibitors of the acute pancreatitis target kynurenine-3-monooxygenase.
Authors: Hutchinson, J.P. / Rowland, P. / Taylor, M.R.D. / Christodoulou, E.M. / Haslam, C. / Hobbs, C.I. / Holmes, D.S. / Homes, P. / Liddle, J. / Mole, D.J. / Uings, I. / Walker, A.L. / Webster, S. ...Authors: Hutchinson, J.P. / Rowland, P. / Taylor, M.R.D. / Christodoulou, E.M. / Haslam, C. / Hobbs, C.I. / Holmes, D.S. / Homes, P. / Liddle, J. / Mole, D.J. / Uings, I. / Walker, A.L. / Webster, S.P. / Mowat, C.G. / Chung, C.W.
History
DepositionFeb 27, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kynurenine 3-monooxygenase
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8706
Polymers101,5752
Non-polymers2,2954
Water14,844824
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9353
Polymers50,7881
Non-polymers1,1472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9353
Polymers50,7881
Non-polymers1,1472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)69.870, 51.980, 136.020
Angle α, β, γ (deg.)90.00, 103.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kynurenine 3-monooxygenase / / PfKMO / Kynurenine 3-hydroxylase


Mass: 50787.516 Da / Num. of mol.: 2 / Mutation: C252S C461S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG / Production host: Escherichia coli (E. coli) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase
#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-8RB / 3-[5-chloranyl-6-[(1~{R})-1-(6-methylpyridazin-3-yl)ethoxy]-1,2-benzoxazol-3-yl]propanoic acid


Mass: 361.780 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H16ClN3O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 824 / 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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% glycerol, 14.4% PEG 8000, 0.08 M sodium cacodylate pH 6.5, 0.16 M calcium acetate or 20% glycerol, 16% PEG 8000, 0.08M sodium cacodylate pH 6.5, 0.16M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.75→49 Å / Num. obs: 95918 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 29.61 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Net I/σ(I): 13.4
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 9341 / CC1/2: 0.611 / % possible all: 99.7

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→44.05 Å / Cor.coef. Fo:Fc: 0.9621 / Cor.coef. Fo:Fc free: 0.9518 / SU R Cruickshank DPI: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.2033 3774 3.94 %RANDOM
Rwork0.1756 ---
obs0.1767 95896 99.74 %-
Displacement parametersBiso mean: 38.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.0753 Å20 Å2-1.1249 Å2
2---1.2313 Å20 Å2
3----0.844 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å
Refinement stepCycle: 1 / Resolution: 1.75→44.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6991 0 156 824 7971
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0097339HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9610009HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2534SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes183HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1210HARMONIC5
X-RAY DIFFRACTIONt_it7339HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion936SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9384SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 259 3.67 %
Rwork0.2334 6795 -
all0.2343 7054 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.68740.14030.01580.77860.03990.5635-0.03850.0523-0.0004-0.122200.053-0.0641-0.02720.0385-0.05440.0162-0.0133-0.0479-0.0268-0.07385.9808-37.47250.3912
20.9574-0.1672-0.13310.8594-0.02290.5142-0.0729-0.1576-0.01440.17520.0554-0.0066-0.04270.05340.0175-0.05780.00270.0011-0.07740.0105-0.0771-21.7304-8.574315.9902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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