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

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Basic information

Entry
Database: PDB / ID: 5mzi
TitlePseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with 3-(5-chloro-6-cyclopropoxy-2-oxo-2,3-dihydro-1,3-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 / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process / L-tryptophan catabolic process / NAD+ metabolic process / NAD+ biosynthetic 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 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-FYK / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.71 Å
AuthorsRowland, P.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Development of a Series of Kynurenine 3-Monooxygenase Inhibitors Leading to a Clinical Candidate for the Treatment of Acute Pancreatitis.
Authors: Walker, A.L. / Ancellin, N. / Beaufils, B. / Bergeal, M. / Binnie, M. / Bouillot, A. / Clapham, D. / Denis, A. / Haslam, C.P. / Holmes, D.S. / Hutchinson, J.P. / Liddle, J. / McBride, A. / ...Authors: Walker, A.L. / Ancellin, N. / Beaufils, B. / Bergeal, M. / Binnie, M. / Bouillot, A. / Clapham, D. / Denis, A. / Haslam, C.P. / Holmes, D.S. / Hutchinson, J.P. / Liddle, J. / McBride, A. / Mirguet, O. / Mowat, C.G. / Rowland, P. / Tiberghien, N. / Trottet, L. / Uings, I. / Webster, S.P. / Zheng, X. / Mole, D.J.
History
DepositionJan 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)104,79413
Polymers101,4792
Non-polymers3,31511
Water13,691760
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5467
Polymers50,7401
Non-polymers1,8066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2486
Polymers50,7401
Non-polymers1,5085
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.580, 52.970, 136.140
Angle α, β, γ (deg.)90.00, 103.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 50739.520 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

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Non-polymers , 5 types, 771 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FYK / 3-(5-chloro-6-cyclopropoxy-2-oxo-2,3-dihydro-1,3-benzoxazol-3-yl)propanoic acid


Mass: 297.691 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C13H12ClNO5
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 760 / 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: 2.4 Å3/Da / Density % sol: 48.75 %
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: ID29 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.71→45 Å / Num. obs: 100649 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 26.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 10.7
Reflection shellResolution: 1.71→1.77 Å / Redundancy: 3 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 8226 / CC1/2: 0.467 / % possible all: 82.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.71→34.2 Å / Cor.coef. Fo:Fc: 0.9605 / Cor.coef. Fo:Fc free: 0.9543 / SU R Cruickshank DPI: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.107 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.094
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 4942 4.91 %RANDOM
Rwork0.1742 ---
obs0.1752 100601 96.32 %-
Displacement parametersBiso mean: 31.65 Å2
Baniso -1Baniso -2Baniso -3
1-0.9517 Å20 Å21.7992 Å2
2---2.6016 Å20 Å2
3---1.6499 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.71→34.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6981 0 220 760 7961
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017374HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9510053HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2551SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1230HARMONIC5
X-RAY DIFFRACTIONt_it7374HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion15.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion932SEMIHARMONIC5
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_contact9073SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2552 239 4.55 %
Rwork0.243 5012 -
all0.2436 5251 -
obs--68.58 %
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)
10.45780.07010.01230.42340.01950.4576-0.02080.0376-0.0233-0.04460.00650.0173-0.0417-0.0060.0143-0.05530.015-0.0241-0.0438-0.0246-0.03275.592-37.917950.3519
20.5918-0.0553-0.010.4733-0.01370.3354-0.0565-0.0671-0.03170.08770.0457-0.0041-0.03770.00040.0108-0.05130.0198-0.0148-0.05210.0109-0.0336-21.6737-8.107515.8755
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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