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- PDB-9az8: Kynurenine monooxygenase from Pseudomonas fluorescens complexed w... -

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Basic information

Entry
Database: PDB / ID: 9az8
TitleKynurenine monooxygenase from Pseudomonas fluorescens complexed with 4-cyclohexylphenylacetyltetrazole
ComponentsKynurenine 3-monooxygenase
KeywordsFLAVOPROTEIN/INHIBITOR / inhibition / bioisostere / monooxygenase / tryptophan metabolism / FLAVOPROTEIN / FLAVOPROTEIN-INHIBITOR complex
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 superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPhillips, R.S. / Ma, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Kynurenine monooxygenase from Pseudomonas fluorescens complexed with 4-cyclohexylphenylacetyltetrazole
Authors: Phillips, R.S. / Ma, W.
History
DepositionMar 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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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)103,77510
Polymers101,4792
Non-polymers2,2968
Water7,494416
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8665
Polymers50,7401
Non-polymers1,1274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9095
Polymers50,7401
Non-polymers1,1694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.540, 52.540, 136.510
Angle α, β, γ (deg.)90.00, 104.11, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 BL21(DE3) (bacteria) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase

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Non-polymers , 5 types, 424 molecules

#2: Chemical ChemComp-A1AIN / 1-(4-cyclohexylphenyl)-2-(2H-tetrazol-5-yl)ethan-1-one


Mass: 270.330 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H18N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: 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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Details

Has ligand of interestY
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 13% PEG 8000, 0.13M Ca(OAc)2, 14% glycerol, and 0.08M sodium cacodylate pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.8 Å / Num. obs: 129564 / % possible obs: 97.34 % / Redundancy: 1.7 % / Biso Wilson estimate: 41.58 Å2 / CC1/2: 0.997 / Net I/σ(I): 2.56
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 172 / CC1/2: 0.876

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
autoPROCdata processing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→41.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2106 2015 2.95 %
Rwork0.1695 --
obs0.1707 68209 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7094 0 41 417 7552
Refine LS restraintsType: f_chiral_restr / Dev ideal: 0.064 / Number: 1117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-20.32871330.31284497X-RAY DIFFRACTION94
2-2.050.34851460.29724757X-RAY DIFFRACTION99
2.05-2.110.34351410.284785X-RAY DIFFRACTION99
2.11-2.180.3251440.25814789X-RAY DIFFRACTION99
2.18-2.260.30231440.23414752X-RAY DIFFRACTION99
2.26-2.350.26181480.21424767X-RAY DIFFRACTION99
2.35-2.460.25311480.20384771X-RAY DIFFRACTION99
2.46-2.590.24681430.19484780X-RAY DIFFRACTION98
2.59-2.750.26641440.18954748X-RAY DIFFRACTION97
2.75-2.960.25411420.18494522X-RAY DIFFRACTION94
2.96-3.260.2341420.17984811X-RAY DIFFRACTION98
3.26-3.730.21651450.14174739X-RAY DIFFRACTION97
3.73-4.70.15961460.12574715X-RAY DIFFRACTION96
4.7-41.90.1481490.14574761X-RAY DIFFRACTION94
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)
10.6242-0.9788-0.46423.52781.32121.6331-0.00790.0430.0477-0.16090.011-0.0002-0.0839-0.0516-0.03420.2018-0.0248-0.0360.28150.01730.2766-3.4996-4.1109-64.8997
22.6961-0.9572-1.33741.63220.37891.9011-0.1435-0.2689-0.24190.27460.11140.16890.03290.03530.04770.2499-0.027-0.05160.28410.02730.3482-12.5524-4.1341-49.8169
30.8962-0.5814-0.29641.94020.6932.0618-0.0649-0.44260.21410.29290.1076-0.1587-0.19050.1998-0.05530.3756-0.001-0.07490.4726-0.05150.47952.44050.6968-47.5186
44.70171.88851.23015.05434.43696.7853-0.1148-0.2750.4885-0.18770.1553-0.1523-0.76920.2855-0.15150.6199-0.0445-0.07510.5041-0.07360.59475.321118.3444-38.6191
50.5848-0.73611.0884.5177-1.60292.0361-0.0434-0.10920.12380.13970.02390.0003-0.05080.07730.01770.2691-0.0014-0.02870.2863-0.05560.213519.478214.3445-0.9605
68.41370.4934-5.17764.427-1.09376.50670.30120.34470.5959-0.0582-0.2751-0.0155-0.5958-0.4126-0.07880.31520.0266-0.08990.259-0.04070.282927.095235.7183-11.2902
72.3532.46470.50886.62830.2392.2961-0.0794-0.1189-0.2370.02630.0558-0.19860.2558-0.05120.02110.2040.0497-0.00390.3264-0.02730.281617.83818.4452-3.1568
82.98010.952-0.80291.0765-0.35451.039-0.06730.2168-0.1472-0.17520.0275-0.08330.0517-0.0560.05410.34960.0143-0.02540.2736-0.03680.26228.298419.3845-19.8713
90.29940.01190.56385.4339-2.99562.7291-0.06270.28640.4194-0.0515-0.1425-0.3911-0.47120.05240.17490.51040.0305-0.0710.493-0.03840.490515.597734.3435-22.5532
103.10532.8854-3.06234.5589-5.41486.5394-0.43840.93560.1882-0.00970.6169-0.4762-0.511-1.0995-0.12260.70510.0319-0.04380.8334-0.09340.625811.506344.8575-30.9921
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 286 )
3X-RAY DIFFRACTION3chain 'A' and (resid 287 through 395 )
4X-RAY DIFFRACTION4chain 'A' and (resid 396 through 457 )
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 105 )
7X-RAY DIFFRACTION7chain 'B' and (resid 106 through 170 )
8X-RAY DIFFRACTION8chain 'B' and (resid 171 through 343 )
9X-RAY DIFFRACTION9chain 'B' and (resid 344 through 413 )
10X-RAY DIFFRACTION10chain 'B' and (resid 414 through 457 )

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