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- PDB-4j34: Crystal Structure of kynurenine 3-monooxygenase - truncated at po... -

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Basic information

Entry
Database: PDB / ID: 4j34
TitleCrystal Structure of kynurenine 3-monooxygenase - truncated at position 394 plus HIS tag cleaved.
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / Monooxygenase kynurenine HIS cleaved
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 (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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)91,3224
Polymers89,7512
Non-polymers1,5712
Water7,494416
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6612
Polymers44,8751
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)45,6612
Polymers44,8751
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.070, 98.780, 86.300
Angle α, β, γ (deg.)90.000, 105.770, 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: 44875.410 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.58 Å3/Da / Density % sol: 52.23 %
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 , VAPOR DIFFUSION, ...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 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→56.8 Å / Num. all: 244828 / Num. obs: 60736

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
GDAdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→56.8 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / σ(F): 0 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2411 2944 5.04 %
Rwork0.2012 --
obs0.2032 58403 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.96 Å2 / Biso mean: 42.7304 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: LAST / Resolution: 2.03→56.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6106 0 106 416 6628

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