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- PDB-5nak: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in compl... -

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Basic information

Entry
Database: PDB / ID: 5nak
TitlePseudomonas fluorescens kynurenine 3-monooxygenase (KMO) in complex with the enzyme substrate L-kynurenine
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / KMO
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
FLAVIN-ADENINE DINUCLEOTIDE / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsTaylor, M. / Mowat, C.G. / Rowland, P.
CitationJournal: Nat Commun / Year: 2017
Title: Structural and mechanistic basis of differentiated inhibitors of the acute pancreatitis target kynurenine-3-monooxygenase.
Authors: Hutchinson, J.P. / Rowland, P. / Taylor, M.R.D. / Christodoulou, E.M. / Haslam, C. / Hobbs, C.I. / Holmes, D.S. / Homes, P. / Liddle, J. / Mole, D.J. / Uings, I. / Walker, A.L. / Webster, S. ...Authors: Hutchinson, J.P. / Rowland, P. / Taylor, M.R.D. / Christodoulou, E.M. / Haslam, C. / Hobbs, C.I. / Holmes, D.S. / Homes, P. / Liddle, J. / Mole, D.J. / Uings, I. / Walker, A.L. / Webster, S.P. / Mowat, C.G. / Chung, C.W.
History
DepositionFeb 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kynurenine 3-monooxygenase
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5139
Polymers101,4792
Non-polymers2,0347
Water19,5281084
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-46 kcal/mol
Surface area39600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.930, 52.620, 137.990
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 50739.520 Da / Num. of mol.: 2 / Mutation: C252S C461S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG / Production host: Escherichia coli (E. coli) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase

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Non-polymers , 5 types, 1091 molecules

#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1084 / 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: 2.43 Å3/Da / Density % sol: 49.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% glycerol, 11.0% PEG 8000, 0.08 M sodium cacodylate pH 7.0, 0.16 M calcium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.5→68 Å / Num. obs: 155570 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.83 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 8.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 22560 / CC1/2: 0.495 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
iMOSFLMdata reduction
SCALAdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→67.48 Å / Cor.coef. Fo:Fc: 0.9626 / Cor.coef. Fo:Fc free: 0.9562 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.078 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.072
RfactorNum. reflection% reflectionSelection details
Rfree0.2104 7716 4.96 %RANDOM
Rwork0.1885 ---
obs0.1896 155537 99.66 %-
Displacement parametersBiso mean: 29.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.2415 Å20 Å2-0.5449 Å2
2---1.051 Å20 Å2
3---0.8095 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.5→67.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7003 0 135 1084 8222
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017304HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969947HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2542SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1174HARMONIC5
X-RAY DIFFRACTIONt_it7304HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.08
X-RAY DIFFRACTIONt_other_torsion16.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion934SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8279SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2644 515 4.52 %
Rwork0.2458 10873 -
all0.2467 11388 -
obs--99.56 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4732-0.05690.08260.4341-0.02640.3877-0.0328-0.0071-0.03150.07390.02080.025-0.0136-0.05020.012-0.0512-0.00470.0106-0.03640.0113-0.039413.11480.603116.2557
20.50970.0524-0.02170.4627-0.01010.3815-0.0348-0.02530.0142-0.10080.02090.0076-0.02880.00990.0139-0.0302-0.0161-0.0021-0.0177-0.0258-0.088840.293224.578250.9614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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