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- PDB-5n7t: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in compl... -

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Basic information

Entry
Database: PDB / ID: 5n7t
TitlePseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with 3-(5,6-dichloro-2-oxo-2,3-dihydro-1,3-benzoxazol-3-yl)propanoic acid
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / KMO / kynurenine 3-monooxygenase
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+ biosynthetic 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 / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-JHY / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.81 Å
AuthorsRowland, P.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: The discovery of potent and selective kynurenine 3-monooxygenase inhibitors for the treatment of acute pancreatitis.
Authors: Liddle, J. / Beaufils, B. / Binnie, M. / Bouillot, A. / Denis, A.A. / Hann, M.M. / Haslam, C.P. / Holmes, D.S. / Hutchinson, J.P. / Kranz, M. / McBride, A. / Mirguet, O. / Mole, D.J. / ...Authors: Liddle, J. / Beaufils, B. / Binnie, M. / Bouillot, A. / Denis, A.A. / Hann, M.M. / Haslam, C.P. / Holmes, D.S. / Hutchinson, J.P. / Kranz, M. / McBride, A. / Mirguet, O. / Mole, D.J. / Mowat, C.G. / Pal, S. / Rowland, P. / Trottet, L. / Uings, I.J. / Walker, A.L. / Webster, S.P.
History
DepositionFeb 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1May 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)104,41016
Polymers101,4792
Non-polymers2,93114
Water16,808933
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2058
Polymers50,7401
Non-polymers1,4657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2058
Polymers50,7401
Non-polymers1,4657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.730, 53.110, 136.490
Angle α, β, γ (deg.)90.00, 103.81, 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, 947 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-JHY / 3-(5,6-DICHLORO-2-OXOBENZO[D]OXAZOL-3(2H)-YL)PROPANOIC ACID


Mass: 276.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7Cl2NO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 933 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
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: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.81→133 Å / Num. obs: 88690 / % possible obs: 99.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 27.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Net I/σ(I): 14.3
Reflection shellResolution: 1.81→1.81 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.61 / Num. unique obs: 887 / CC1/2: 0.697 / % possible all: 99.2

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.81→132.55 Å / Cor.coef. Fo:Fc: 0.9617 / Cor.coef. Fo:Fc free: 0.9542 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.103
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 3491 3.96 %RANDOM
Rwork0.1633 ---
obs0.1642 88180 99.15 %-
Displacement parametersBiso mean: 35.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.3889 Å20 Å2-1.4195 Å2
2---4.282 Å20 Å2
3---3.8931 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: 1 / Resolution: 1.81→132.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6993 0 190 933 8116
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.959994HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2546SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1165HARMONIC5
X-RAY DIFFRACTIONt_it7343HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion16.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion935SEMIHARMONIC5
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_contact9117SEMIHARMONIC4
LS refinement shellResolution: 1.81→1.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2277 271 4.17 %
Rwork0.2204 6222 -
all0.2207 6493 -
obs--99.28 %
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)
10.68880.1384-0.03890.57-0.02950.4854-0.03060.06270.0141-0.09890.01130.0385-0.0358-0.00220.0194-0.04750.0097-0.03-0.0664-0.0229-0.04695.6813-37.862450.6454
20.8345-0.1433-0.14720.7055-0.03640.6011-0.0678-0.1253-0.04870.13140.0821-0.0278-0.04650.0234-0.0143-0.05560.0189-0.0194-0.05750.0118-0.0739-21.7789-8.091115.9378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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