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- PDB-5na5: Pseudomonas fluorescens kynurenine 3-monooxygenase (KMO) apo structure -

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Basic information

Entry
Database: PDB / ID: 5na5
TitlePseudomonas fluorescens kynurenine 3-monooxygenase (KMO) apo structure
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 / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.94 Å
AuthorsRowland, 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 27, 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)103,3058
Polymers101,4792
Non-polymers1,8266
Water11,025612
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6534
Polymers50,7401
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6534
Polymers50,7401
Non-polymers9133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.430, 53.740, 137.560
Angle α, β, γ (deg.)90.00, 103.64, 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: 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
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% glycerol, 14.4% PEG 8000, 0.08 M sodium cacodylate pH 6.5, 0.16 M calcium acetate or 20% glycerol, 16% PEG 8000, 0.08M sodium cacodylate pH 6.5, 0.16M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.94→134 Å / Num. obs: 71621 / % possible obs: 96.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 27.72 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.052 / Net I/σ(I): 16.9
Reflection shellResolution: 1.94→1.98 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 3201 / CC1/2: 0.542 / % possible all: 86.4

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.94→133.68 Å / Cor.coef. Fo:Fc: 0.9389 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.178 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2854 3.99 %RANDOM
Rwork0.2007 ---
obs0.2019 71566 96.01 %-
Displacement parametersBiso mean: 33.85 Å2
Baniso -1Baniso -2Baniso -3
1--3.7868 Å20 Å20.0711 Å2
2--1.2706 Å20 Å2
3---2.5162 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: 1 / Resolution: 1.94→133.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6993 0 120 612 7725
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017277HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.969912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2524SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes182HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1159HARMONIC5
X-RAY DIFFRACTIONt_it7277HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion17.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion935SEMIHARMONIC5
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_contact7811SEMIHARMONIC4
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3231 178 3.8 %
Rwork0.28 4502 -
all0.2817 4680 -
obs--85.46 %
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)
10.60620.1233-0.03440.6889-0.02950.5246-0.04260.0539-0.0283-0.12690.01190.0158-0.03520.01520.0308-0.0820.003-0.02490.0103-0.0318-0.06995.9252-38.028251.0428
21.1033-0.3493-0.20930.7159-0.05631.0392-0.0585-0.1272-0.06550.0660.1169-0.0299-0.0628-0.0455-0.0584-0.14050.0105-0.00970.00520.0262-0.112-21.9162-8.092516.07
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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