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- PDB-5x6r: Crystal structure of Saccharomyces cerevisiae KMO in complex with... -

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Basic information

Entry
Database: PDB / ID: 5x6r
TitleCrystal structure of Saccharomyces cerevisiae KMO in complex with Ro 61-8048
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / monooxygenase
Function / homology
Function and homology information


Tryptophan catabolism / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / anthranilate metabolic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process / L-tryptophan catabolic process / NAD+ metabolic process ...Tryptophan catabolism / kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / anthranilate metabolic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process / L-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-7ZR / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.911 Å
AuthorsKim, H.T. / Hwang, K.Y.
CitationJournal: Cell Chem Biol / Year: 2018
Title: Structural Basis for Inhibitor-Induced Hydrogen Peroxide Production by Kynurenine 3-Monooxygenase
Authors: Kim, H.T. / Na, B.K. / Chung, J. / Kim, S. / Kwon, S.K. / Cha, H. / Son, J. / Cho, J.M. / Hwang, K.Y.
History
DepositionFeb 23, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed
Revision 1.2May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)98,2416
Polymers95,8272
Non-polymers2,4144
Water6,341352
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1213
Polymers47,9141
Non-polymers1,2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7 kcal/mol
Surface area17180 Å2
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1213
Polymers47,9141
Non-polymers1,2072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-6 kcal/mol
Surface area16600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.878, 99.764, 84.693
Angle α, β, γ (deg.)90.00, 105.45, 90.00
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: 47913.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-394
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: BNA4, YBL098W, YBL0828
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
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-7ZR / 3,4-dimethoxy-N-[4-(3-nitrophenyl)-1,3-thiazol-2-yl]benzenesulfonamide / Ro 61-8048


Mass: 421.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H15N3O6S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 0.1 M NaCl, and 12% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CCD / Date: Dec 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→30.797 Å / Num. obs: 72243 / % possible obs: 99.03 % / Redundancy: 3.6 % / Net I/σ(I): 27.19
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.16 / Num. unique obs: 3550 / CC1/2: 0.899 / Rpim(I) all: 0.24 / Rrim(I) all: 0.438 / Rsym value: 0.364 / Χ2: 1.674 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J33

4j33


Resolution: 1.911→30.797 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.85
RfactorNum. reflection% reflection
Rfree0.2597 1993 2.76 %
Rwork0.2112 --
obs0.2125 72243 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.911→30.797 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 162 352 6375
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096176
X-RAY DIFFRACTIONf_angle_d1.1378348
X-RAY DIFFRACTIONf_dihedral_angle_d14.982355
X-RAY DIFFRACTIONf_chiral_restr0.049900
X-RAY DIFFRACTIONf_plane_restr0.0051131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9112-1.9590.39651610.36364924X-RAY DIFFRACTION98
1.959-2.0120.36661340.3155003X-RAY DIFFRACTION100
2.012-2.07120.31531410.27075076X-RAY DIFFRACTION100
2.0712-2.1380.29111350.25395058X-RAY DIFFRACTION100
2.138-2.21440.32081530.26795011X-RAY DIFFRACTION100
2.2144-2.3030.31281370.25545071X-RAY DIFFRACTION100
2.303-2.40780.33251400.25985047X-RAY DIFFRACTION100
2.4078-2.53470.27561520.23275050X-RAY DIFFRACTION100
2.5347-2.69340.27441530.23175057X-RAY DIFFRACTION100
2.6934-2.90120.25021350.23135068X-RAY DIFFRACTION100
2.9012-3.19290.25951450.22145052X-RAY DIFFRACTION100
3.1929-3.65430.26441310.20294868X-RAY DIFFRACTION96
3.6543-4.60160.21991390.16615057X-RAY DIFFRACTION99
4.6016-30.80120.21861370.17374908X-RAY DIFFRACTION95

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