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- PDB-9b2y: Kynurenine monooxygenase from Pseudomonas fluorescens complexed w... -

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Basic information

Entry
Database: PDB / ID: 9b2y
TitleKynurenine monooxygenase from Pseudomonas fluorescens complexed with 4-chlorophenylacetyltetrazole
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: 2.05 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-chlorophenylacetyltetrazole
Authors: Phillips, R.S. / Ma, W.
History
DepositionMar 17, 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)103,3086
Polymers101,4792
Non-polymers1,8294
Water4,468248
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5252
Polymers50,7401
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7834
Polymers50,7401
Non-polymers1,0443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.410, 51.660, 134.980
Angle α, β, γ (deg.)90.00, 103.86, 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

#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
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-A1AI5 / 1-(3-chlorophenyl)-2-(2H-tetrazol-5-yl)ethan-1-one


Mass: 222.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClN4O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12%-14% PEG8k, 0.11M - 0.13M calcium acetate, 14% glycerol, 0.08M sodium cacodylate pH6

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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: Apr 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→43.68 Å / Num. obs: 104865 / % possible obs: 93.68 % / Redundancy: 2.3 % / Biso Wilson estimate: 50.67 Å2
Data reduction details: The depositor states that the number cited as the number of reflections (104865) must have come from the data file before application of the resolution cutoff.
CC1/2: 0.998 / Net I/σ(I): 6.09
Reflection shellResolution: 2.05→2.1 Å / Num. unique obs: 7765 / CC1/2: 0.176

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→43.68 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 2022 3.67 %
Rwork0.2054 --
obs0.2069 55104 93.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→43.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7104 0 0 249 7353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d11.7552827
X-RAY DIFFRACTIONf_chiral_restr0.0421109
X-RAY DIFFRACTIONf_plane_restr0.0061337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10.45381380.41473659X-RAY DIFFRACTION91
2.1-2.160.38461520.37283842X-RAY DIFFRACTION96
2.16-2.220.37131370.34313864X-RAY DIFFRACTION96
2.22-2.290.40421460.34313840X-RAY DIFFRACTION96
2.29-2.380.38561480.31053831X-RAY DIFFRACTION95
2.38-2.470.30171480.26553876X-RAY DIFFRACTION95
2.47-2.580.33321420.25293797X-RAY DIFFRACTION95
2.58-2.720.24791510.24683787X-RAY DIFFRACTION94
2.72-2.890.27131370.24393724X-RAY DIFFRACTION92
2.89-3.110.2521440.22483845X-RAY DIFFRACTION96
3.11-3.430.2671470.20513844X-RAY DIFFRACTION95
3.43-3.920.24641420.17183795X-RAY DIFFRACTION93
3.92-4.940.1731420.14943640X-RAY DIFFRACTION89
4.94-43.680.20541480.17013738X-RAY DIFFRACTION89
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)
10.2884-0.8258-0.56393.71371.17441.5999-0.0549-0.0478-0.0121-0.09640.0195-0.1947-0.07660.09020.02590.3254-0.0109-0.04190.46250.05040.4012-3.9285-4.7875-64.0912
22.1576-0.8883-0.98761.52930.35971.3696-0.1768-0.3698-0.33920.31350.1050.21020.05560.1020.08860.4198-0.01-0.02390.50350.07630.4896-12.7438-4.8646-49.4811
30.5717-0.8446-0.30113.10992.08413.0375-0.083-0.26890.24170.33390.0592-0.1076-0.420.19030.00260.6345-0.0363-0.07870.74390.00770.65743.15036.7204-43.5604
40.0634-0.11420.38083.4564-0.51732.2006-0.0814-0.2295-0.04030.01770.05060.07020.07110.06160.02870.33790.0105-0.04290.4035-0.01240.348919.568713.7687-0.9379
56.99261.7165-4.92134.3053-2.81618.18080.31130.12510.5726-0.0006-0.2006-0.0274-0.7293-0.0974-0.19360.4637-0.0133-0.05750.3058-0.05930.393426.867635.0187-11.2035
62.05921.12480.23584.07710.55122.0395-0.0128-0.0085-0.32560.21290.0049-0.18660.152-0.07990.04470.33250.0284-0.04950.4718-0.01650.467717.89257.836-3.178
72.19870.1775-0.54760.7948-0.11361.4966-0.1180.2459-0.2138-0.32930.0584-0.08270.0331-0.05940.05450.4665-0.0055-0.01030.3552-0.0460.365532.31318.2269-22.0202
84.06670.2008-1.02311.4215-0.5652.21870.0150.20040.21-0.20860.00030.0903-0.2448-0.0065-0.05390.5194-0.0065-0.10780.53280.01520.521611.195420.998-14.7391
92.7302-1.22971.01979.0007-5.22927.3507-0.31190.49380.2549-0.4937-0.0678-0.4803-0.3137-0.03690.29510.76580.1061-0.08520.7711-0.01830.722115.910939.9767-26.2673
102.6642-0.4093-0.00438.7986-4.90112.7430.4151.53281.2178-0.58080.16750.4197-1.7055-1.1454-0.32971.25230.2246-0.23841.18680.08770.80811.694549.5865-32.2715
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 457 )
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 58 )
5X-RAY DIFFRACTION5chain 'B' and (resid 59 through 105 )
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 170 )
7X-RAY DIFFRACTION7chain 'B' and (resid 171 through 305 )
8X-RAY DIFFRACTION8chain 'B' and (resid 306 through 373 )
9X-RAY DIFFRACTION9chain 'B' and (resid 374 through 432 )
10X-RAY DIFFRACTION10chain 'B' and (resid 433 through 457 )

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