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- PDB-4j2w: Crystal Structure of kynurenine 3-monooxygenase (KMO-396Prot-Se) -

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Basic information

Entry
Database: PDB / ID: 4j2w
TitleCrystal Structure of kynurenine 3-monooxygenase (KMO-396Prot-Se)
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase
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 / 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
FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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)96,1854
Polymers94,6142
Non-polymers1,5712
Water1,928107
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0932
Polymers47,3071
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)48,0932
Polymers47,3071
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.130, 99.400, 85.360
Angle α, β, γ (deg.)90.000, 105.610, 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: 47307.090 Da / Num. of mol.: 2 / Fragment: unp residues 1-396 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38169, 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN IS PROTEOLYTICALLY CLEAVED DURING PURIFICATION AT RESIDUE 396.

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Initial crystals of Saccharomyces cerevisiae KMO KMO-396Prot-Se were obtained by mixing 200 nl of 14 mg/ml protein in 20 mM ammonium acetate, pH 7.0, 150 mM NaCl and 7 mM 2-mercaptoethanol ...Details: Initial crystals of Saccharomyces cerevisiae KMO KMO-396Prot-Se were obtained by mixing 200 nl of 14 mg/ml protein in 20 mM ammonium acetate, pH 7.0, 150 mM NaCl and 7 mM 2-mercaptoethanol (buffer A) with 200 nl of a reservoir solution containing 0.1 M sodium acetate, pH 5.5, and 35 % isopropanol. , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→38.6 Å / Num. all: 226969 / Num. obs: 29704 / % possible obs: 99.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.755 / Mean I/σ(I) obs: 2.1 / % possible all: 98.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
SOLVEphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→38.6 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 0 / Phase error: 29.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 1454 5.06 %
Rwork0.1982 --
obs0.2013 28736 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.86 Å2 / Biso mean: 26.2173 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→38.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6035 0 106 107 6248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096271
X-RAY DIFFRACTIONf_angle_d1.2778469
X-RAY DIFFRACTIONf_chiral_restr0.088925
X-RAY DIFFRACTIONf_plane_restr0.0051073
X-RAY DIFFRACTIONf_dihedral_angle_d15.9182358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.58-2.67220.35991260.27282512263888
2.6722-2.77920.31791320.25982532266490
2.7792-2.90560.32821210.25062687280894
2.9056-3.05870.35521390.26142693283295
3.0587-3.25030.29751550.2452731288697
3.2503-3.50110.35131300.22272816294698
3.5011-3.85310.26031710.19092783295499
3.8531-4.410.24811650.16992798296399
4.41-5.55350.20871550.16192853300899
5.5535-38.630.20111600.17612877303799

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