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- PDB-9b07: Kynurenine monooxygenase from Pseudomonas fluorescens complexed w... -

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Basic information

Entry
Database: PDB / ID: 9b07
TitleKynurenine monooxygenase from Pseudomonas fluorescens complexed with biphenylacetyltetrazole
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: 1.88 Å
AuthorsPhillips, R.S. / Ma, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Inhibition of kynurenine monooxygenase by tetrazoles
Authors: Phillips, R.S. / Ma, W.
History
DepositionMar 11, 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)103,7289
Polymers101,4792
Non-polymers2,2497
Water8,557475
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8254
Polymers50,7401
Non-polymers1,0853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9035
Polymers50,7401
Non-polymers1,1634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.050, 52.190, 135.880
Angle α, β, γ (deg.)90.00, 103.70, 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, 482 molecules

#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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-A1AIU / 1-([1,1'-biphenyl]-4-yl)-2-(2H-tetrazol-5-yl)ethan-1-one


Mass: 264.282 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12N4O / Feature type: SUBJECT OF INVESTIGATION
#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.: 475 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 13% PEG 8000, 0.13M Ca(OAc)2, 14% glycerol, and 0.08 M sodium cacodylate, pH 6.5

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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: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→55.38 Å / Num. obs: 76842 / % possible obs: 98.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.95 Å2 / CC1/2: 0.999 / Net I/σ(I): 9.91
Reflection shellResolution: 1.88→1.93 Å / Num. unique obs: 5691 / CC1/2: 0.281

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→55.38 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 2003 2.61 %
Rwork0.194 --
obs0.1949 76623 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→55.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 152 475 7609
Refine LS restraintsType: f_dihedral_angle_d / Dev ideal: 11.686 / Number: 2867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.930.37811430.39725226X-RAY DIFFRACTION97
1.93-1.980.37271440.36535307X-RAY DIFFRACTION99
1.98-2.040.32981440.34015332X-RAY DIFFRACTION99
2.04-2.10.35551420.30395321X-RAY DIFFRACTION98
2.1-2.180.30711370.27425272X-RAY DIFFRACTION97
2.18-2.270.28631400.24675224X-RAY DIFFRACTION97
2.27-2.370.26491440.22845386X-RAY DIFFRACTION100
2.37-2.490.26941480.22145388X-RAY DIFFRACTION99
2.49-2.650.28381430.21055359X-RAY DIFFRACTION99
2.65-2.850.25471410.20415367X-RAY DIFFRACTION99
2.85-3.140.24441380.20055260X-RAY DIFFRACTION97
3.14-3.60.1781410.17415348X-RAY DIFFRACTION98
3.6-4.530.19841490.15085418X-RAY DIFFRACTION98
4.53-55.380.19871490.1715412X-RAY DIFFRACTION96
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)
10.81120.55110.50043.32690.45741.3066-0.07940.0185-0.1824-0.04330.009-0.1147-0.03120.0110.02730.3507-0.004-0.02370.3110.03370.3625-3.9616-8.5521-65.0322
25.4057-1.4229-3.88082.68330.9553.88080.1258-0.63640.65940.11560.1023-0.2491-0.56870.3728-0.26860.42080.0106-0.0140.3381-0.05260.3863-9.995712.9616-54.5539
32.6654-0.89020.23523.3742-0.35651.3683-0.134-0.1817-0.6631-0.01190.07170.24910.28160.07540.02450.324-0.00310.02560.32730.04780.4467-2.5711-14.3665-63.3695
41.54-0.6578-1.1771.6722-0.03741.4003-0.3433-0.8464-0.48710.63590.41970.30880.09990.0757-0.10260.61840.10060.02070.62460.11650.5052-16.4967-3.3941-43.5553
50.71490.1590.91064.13380.09081.2139-0.1838-0.88490.25451.18130.08790.185-0.1995-0.07610.00080.68330.0352-0.02810.7022-0.10030.59042.01263.586-47.1469
63.67392.74981.43565.7824.19475.3556-0.1635-0.50930.6263-0.47880.43-0.0778-0.99030.334-0.29081.1417-0.1012-0.05311.1527-0.16411.03874.86518.4466-38.3941
70.7406-0.73140.96073.5743-0.70571.78350.001-0.1269-0.03490.0826-0.02150.0742-0.05220.07720.01070.29380.0175-0.01490.3172-0.01960.266519.703514.2188-0.9595
86.29150.3698-3.04883.5567-0.32524.69650.17860.38570.7936-0.2488-0.14980.1547-0.4882-0.3134-0.0390.4080.0203-0.08110.2954-0.00370.35627.116135.6888-11.114
92.30511.41590.58524.69780.31841.6757-0.0145-0.0334-0.31780.08220.0325-0.12440.2738-0.04720.00070.26480.02770.00350.3653-0.02870.335718.0828.3952-3.1779
101.81910.6521-0.20410.9978-0.16660.9163-0.1420.4238-0.227-0.33330.0939-0.02030.0289-0.00580.03770.4189-0.0123-0.01970.4073-0.07350.342228.296919.2754-19.8391
110.84530.345-0.04186.5669-3.2113.1386-0.06740.45060.4551-0.5653-0.0774-0.2018-0.5246-0.07790.10410.80440.0981-0.12460.7177-0.00850.654113.841438.1764-25.6031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 58 )
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 105 )
3X-RAY DIFFRACTION3chain 'A' and (resid 106 through 170 )
4X-RAY DIFFRACTION4chain 'A' and (resid 171 through 305 )
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 395 )
6X-RAY DIFFRACTION6chain 'A' and (resid 396 through 457 )
7X-RAY DIFFRACTION7chain 'B' and (resid 7 through 58 )
8X-RAY DIFFRACTION8chain 'B' and (resid 59 through 105 )
9X-RAY DIFFRACTION9chain 'B' and (resid 106 through 170 )
10X-RAY DIFFRACTION10chain 'B' and (resid 171 through 343 )
11X-RAY DIFFRACTION11chain 'B' and (resid 344 through 457 )

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