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- PDB-5x6q: Crystal structure of Pseudomonas fluorescens KMO in complex with ... -

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Basic information

Entry
Database: PDB / ID: 5x6q
TitleCrystal structure of Pseudomonas fluorescens KMO in complex with Ro 61-8048
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / monoxygenase
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+ metabolic process / NAD+ biosynthetic 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
Chem-7ZR / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5124
Polymers50,8841
Non-polymers1,6283
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-8 kcal/mol
Surface area20440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.537, 45.651, 76.707
Angle α, β, γ (deg.)90.00, 105.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Kynurenine 3-monooxygenase / PfKMO / Kynurenine 3-hydroxylase


Mass: 50883.648 Da / Num. of mol.: 1 / Mutation: C252S,C461S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: Q84HF5, kynurenine 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / 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.: 203 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.08 M sodium cacodylate (pH 6.5), 0.16 M calcium acetate, 14.4% polyethylene glycol 8000, and 20% glycerol

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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: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.897→33.653 Å / Num. obs: 35769 / % possible obs: 97.64 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.047 / Rrim(I) all: 0.084 / Rsym value: 0.069 / Χ2: 2.615 / Net I/σ(I): 30.96
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 1786 / CC1/2: 0.838 / Rpim(I) all: 0.241 / Rrim(I) all: 0.447 / Rsym value: 0.375 / Χ2: 1.048 / % possible all: 99.9

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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: 5FN0

5fn0


Resolution: 1.897→33.653 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.5
RfactorNum. reflection% reflection
Rfree0.2345 1788 5 %
Rwork0.1957 --
obs0.1977 35769 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.897→33.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 109 203 3761
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083641
X-RAY DIFFRACTIONf_angle_d1.1814959
X-RAY DIFFRACTIONf_dihedral_angle_d14.8931357
X-RAY DIFFRACTIONf_chiral_restr0.046541
X-RAY DIFFRACTIONf_plane_restr0.007688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8967-1.9480.30951350.23962563X-RAY DIFFRACTION98
1.948-2.00530.30991410.22722668X-RAY DIFFRACTION100
2.0053-2.070.28091410.20972676X-RAY DIFFRACTION100
2.07-2.1440.27741360.21482608X-RAY DIFFRACTION100
2.144-2.22980.24891400.20542660X-RAY DIFFRACTION100
2.2298-2.33130.29021390.2132650X-RAY DIFFRACTION99
2.3313-2.45410.26521380.21132637X-RAY DIFFRACTION99
2.4541-2.60780.2281390.20752624X-RAY DIFFRACTION98
2.6078-2.80910.27641390.21872628X-RAY DIFFRACTION98
2.8091-3.09160.27451360.2072590X-RAY DIFFRACTION96
3.0916-3.53860.22931330.20142530X-RAY DIFFRACTION94
3.5386-4.45660.20671290.16892468X-RAY DIFFRACTION91
4.4566-33.65790.17671420.17392679X-RAY DIFFRACTION96

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