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- PDB-4j36: Cocrystal Structure of kynurenine 3-monooxygenase in complex with... -

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Basic information

Entry
Database: PDB / ID: 4j36
TitleCocrystal Structure of kynurenine 3-monooxygenase in complex with UPF 648 inhibitor(KMO-394UPF)
ComponentsKynurenine 3-monooxygenase
KeywordsOxidoreductase/Oxidoreductase inhibitor / Monooxygenase kynurenine UPF 648 / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


Tryptophan catabolism / 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 ...Tryptophan catabolism / 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 / peroxisome / flavin adenine dinucleotide binding / mitochondrial outer membrane / mitochondrion
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
Chem-1HR / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsAmaral, M. / Levy, C. / Heyes, D.J. / Lafite, P. / Outeiro, T.F. / Giorgini, F. / Leys, D. / Scrutton, N.S.
CitationJournal: Nature / Year: 2013
Title: Structural basis of kynurenine 3-monooxygenase inhibition.
Authors: Amaral, M. / Levy, C. / Heyes, D.J. / Lafite, P. / Outeiro, T.F. / Giorgini, F. / Leys, D. / Scrutton, N.S.
History
DepositionFeb 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Data collection
Revision 1.2May 1, 2013Group: Database references
Revision 1.3Feb 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

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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)95,9245
Polymers94,0942
Non-polymers1,8303
Water6,467359
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8322
Polymers47,0471
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0913
Polymers47,0471
Non-polymers1,0452
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.970, 89.810, 82.800
Angle α, β, γ (deg.)90.000, 110.600, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kynurenine 3-monooxygenase / Biosynthesis of nicotinic acid protein 4 / Kynurenine 3-hydroxylase


Mass: 47046.762 Da / Num. of mol.: 2 / Fragment: unp residues 1-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: BNA4, YBL098W, YBL0828 / References: UniProt: P38169, kynurenine 3-monooxygenase
#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-1HR / (1S,2S)-2-(3,4-dichlorobenzoyl)cyclopropanecarboxylic acid


Mass: 259.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8Cl2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Crystals were grown by mixing 200 nl of protein (buffer A) with 200 nl of a reservoir solution containing 0.1 M imidazole, pH 7.8, and 11 % w/v polyethylene glycol 8K. The UPF complex (KMO- ...Details: Crystals were grown by mixing 200 nl of protein (buffer A) with 200 nl of a reservoir solution containing 0.1 M imidazole, pH 7.8, and 11 % w/v polyethylene glycol 8K. The UPF complex (KMO-393-UPF) was obtained as described above. However, prior to setting the trays the protein was pre-incubated with 1 mM UPF for ~30 minutes. All trays were incubated at 277 K, with crystals forming over a period of ~72 h , VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1.0725 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0725 Å / Relative weight: 1
ReflectionResolution: 2.1→58.7 Å / Num. all: 167090 / Num. obs: 55595 / Biso Wilson estimate: 39.93 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→58.677 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 1.92 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2386 2820 5.08 %
Rwork0.1978 --
obs0.1999 55563 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.69 Å2 / Biso mean: 13.6611 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.13→58.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 122 359 6257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036026
X-RAY DIFFRACTIONf_angle_d0.7858146
X-RAY DIFFRACTIONf_chiral_restr0.055887
X-RAY DIFFRACTIONf_plane_restr0.0031034
X-RAY DIFFRACTIONf_dihedral_angle_d12.9492258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.16670.34741440.32292624276899
2.1667-2.20620.39021400.32782596273699
2.2062-2.24860.34721260.34232654278099
2.2486-2.29450.37371290.33162625275499
2.2945-2.34440.33581280.270826422770100
2.3444-2.39890.30341400.241926192759100
2.3989-2.45890.2951410.240826382779100
2.4589-2.52540.28481380.242226712809100
2.5254-2.59970.2591460.223826402786100
2.5997-2.68360.28941470.223726312778100
2.6836-2.77950.27031730.22162597277099
2.7795-2.89080.25141610.21482612277399
2.8908-3.02240.26081120.22092638275099
3.0224-3.18170.27261460.21822656280299
3.1817-3.3810.29361340.20452618275299
3.381-3.6420.2121490.1842652280199
3.642-4.00850.21551340.16522636277099
4.0085-4.58830.16031390.13992643278299
4.5883-5.780.19051470.15682653280099
5.78-58.69890.20141460.17352698284499

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