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- PDB-5y77: Crystal structure of Pseudomonas fluorescens Kynurenine 3-monooxy... -

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Basic information

Entry
Database: PDB / ID: 5y77
TitleCrystal structure of Pseudomonas fluorescens Kynurenine 3-monooxygenase in complex with L-KYN (seMet derivative)
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / KMO / L-KYN / enzyme / 3-hydroxy-L-kynurenine (L-3OHKyn)
Function / homology
Function and homology information


kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / quinolinate biosynthetic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / 'de novo' NAD biosynthetic process from tryptophan / tryptophan catabolic process / NAD metabolic 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 / Resolution: 1.6 Å
AuthorsXiang, Y. / Gao, J.J. / Zhu, D.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Beijing Municipal Science & Technology CommissionZ161100000116032 China
CitationJournal: FASEB J. / Year: 2018
Title: Biochemistry and structural studies of kynurenine 3-monooxygenase reveal allosteric inhibition by Ro 61-8048
Authors: Gao, J. / Yao, L. / Xia, T. / Liao, X. / Zhu, D. / Xiang, Y.
History
DepositionAug 16, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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)107,5276
Polymers105,5392
Non-polymers1,9884
Water18,9881054
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7633
Polymers52,7701
Non-polymers9942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area20280 Å2
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7633
Polymers52,7701
Non-polymers9942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-5 kcal/mol
Surface area19810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.555, 52.448, 135.712
Angle α, β, γ (deg.)90.00, 104.33, 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: 52769.598 Da / Num. of mol.: 2
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-KYN / (2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid / L-KYNURENINE


Type: L-peptide linking / Mass: 208.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1054 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46.55 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6
Details: 20% w/v PEG3350, 0.2 M NaCl, 0.1 M Bis-Tris at pH 6.0 and 5 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 232059 / % possible obs: 94.7 % / Redundancy: 3.4 % / Net I/σ(I): 23.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementResolution: 1.6→34.776 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.91
RfactorNum. reflection% reflection
Rfree0.2172 5969 5.01 %
Rwork0.1852 --
obs0.1867 119147 95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→34.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7013 0 136 1054 8203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0187549
X-RAY DIFFRACTIONf_angle_d1.95610321
X-RAY DIFFRACTIONf_dihedral_angle_d14.8722845
X-RAY DIFFRACTIONf_chiral_restr0.1471146
X-RAY DIFFRACTIONf_plane_restr0.011367
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6003-1.61850.23362060.21283821X-RAY DIFFRACTION95
1.6185-1.63750.26881930.20663901X-RAY DIFFRACTION98
1.6375-1.65750.24952030.20233858X-RAY DIFFRACTION99
1.6575-1.67850.22951890.19193879X-RAY DIFFRACTION99
1.6785-1.70050.22962110.19683904X-RAY DIFFRACTION99
1.7005-1.72380.22541910.19453877X-RAY DIFFRACTION99
1.7238-1.74850.2412240.18983953X-RAY DIFFRACTION99
1.7485-1.77460.2262000.18993862X-RAY DIFFRACTION99
1.7746-1.80230.24132130.1933860X-RAY DIFFRACTION99
1.8023-1.83180.23532060.19233898X-RAY DIFFRACTION99
1.8318-1.86340.23762240.2033892X-RAY DIFFRACTION98
1.8634-1.89730.31761920.28413536X-RAY DIFFRACTION90
1.8973-1.93380.28932150.26973930X-RAY DIFFRACTION98
1.9338-1.97330.2292100.23523619X-RAY DIFFRACTION93
1.9733-2.01620.19012000.18463937X-RAY DIFFRACTION99
2.0162-2.06310.22351970.17753955X-RAY DIFFRACTION99
2.0631-2.11460.22861930.17823917X-RAY DIFFRACTION99
2.1146-2.17180.20032020.17333980X-RAY DIFFRACTION99
2.1718-2.23570.22681780.18833343X-RAY DIFFRACTION85
2.2357-2.30780.22411500.20882705X-RAY DIFFRACTION69
2.3078-2.39030.20622120.18173967X-RAY DIFFRACTION99
2.3903-2.4860.23032070.17763958X-RAY DIFFRACTION100
2.486-2.59910.20512190.17463936X-RAY DIFFRACTION100
2.5991-2.73610.21852150.1783957X-RAY DIFFRACTION100
2.7361-2.90740.20422110.17954006X-RAY DIFFRACTION100
2.9074-3.13180.22331860.17583971X-RAY DIFFRACTION100
3.1318-3.44670.19652080.16793982X-RAY DIFFRACTION99
3.4467-3.94480.231910.17522035X-RAY DIFFRACTION50
3.9448-4.96780.16572100.15383857X-RAY DIFFRACTION96
4.9678-34.78430.23152130.19763882X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.3874-0.7393-0.77112.2191-0.00141.2179-0.0524-0.11720.00050.10920.0123-0.13240.03380.02720.0320.0730.0019-0.00450.0633-0.01030.03611.4436.902766.4154
22.02890.25410.56811.99740.34192.5664-0.01010.0234-0.2286-0.1247-0.06020.18910.161-0.26630.04670.17130.0060.03460.1302-0.00240.1644-10.219119.933856.6322
33.30071.23531.99342.7011.31143.2683-0.03650.156-0.2072-0.05070.01590.1460.214-0.0180.06460.0991-0.02260.04910.11260.01570.1001-8.83320.106758.3957
41.00570.45130.16950.73160.24940.6947-0.09230.16320.1377-0.15240.08680.0392-0.0913-0.00380.0180.12770.01070.00160.10750.04190.1086-9.573335.515348.5529
52.68380.38440.9720.59930.08490.7291-0.02680.0352-0.0657-0.11760.03750.01930.0431-0.0547-0.01920.1642-0.0020.02760.13210.01540.1375-0.533229.959449.1793
61.2196-0.7817-0.55132.59212.05571.8415-0.030.2006-0.0911-0.1433-0.21580.17540.1485-0.1590.19490.32720.01720.07970.2145-0.01440.2091.82098.937739.786
71.7048-0.2516-1.08350.3339-0.41632.9059-0.003-0.0979-0.05560.5606-0.08140.28220.84920.4480.06040.57080.12160.10750.334-0.01650.29686.1540.52536.795
81.1150.1957-1.15362.6599-0.5611.4298-0.0150.25540.202-0.0342-0.081-0.1437-0.03290.06250.04510.113-0.0296-0.02220.18540.02820.107620.0347.27360.7414
94.7441-0.5292.86531.4367-0.50544.11250.1946-0.0404-0.7980.0823-0.0137-0.17720.36080.3339-0.19930.24530.0147-0.01320.2159-0.00490.318226.1776-13.794511.7636
101.8117-0.58720.35161.073-0.3310.8563-0.1318-0.03390.28470.16550.1102-0.1513-0.15230.07410.01950.1615-0.0417-0.0110.1586-0.04040.193524.88886.643912.4826
111.8791-0.62140.11021.53770.39611.7745-0.0379-0.20790.16870.2060.2175-0.4375-0.11490.4806-0.0790.1959-0.0571-0.01360.2532-0.08890.248426.10383.748919.3758
120.11780.1953-0.44111.2062-1.2841.7573-0.0707-0.2651-0.32680.034-0.0486-0.04440.27720.15610.16290.28470.00560.06150.18990.00070.238315.3294-9.332823.4888
130.72580.526-0.40892.9125-3.11674.1514-0.0991-0.0927-0.1295-0.23940.04260.11830.4313-0.08460.05540.3542-0.02320.10750.1945-0.0130.262711.6349-19.820827.1538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 91 )
3X-RAY DIFFRACTION3chain 'A' and (resid 92 through 125 )
4X-RAY DIFFRACTION4chain 'A' and (resid 126 through 269 )
5X-RAY DIFFRACTION5chain 'A' and (resid 270 through 374 )
6X-RAY DIFFRACTION6chain 'A' and (resid 375 through 432 )
7X-RAY DIFFRACTION7chain 'A' and (resid 433 through 461 )
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 58 )
9X-RAY DIFFRACTION9chain 'B' and (resid 59 through 105 )
10X-RAY DIFFRACTION10chain 'B' and (resid 106 through 247 )
11X-RAY DIFFRACTION11chain 'B' and (resid 248 through 343 )
12X-RAY DIFFRACTION12chain 'B' and (resid 344 through 395 )
13X-RAY DIFFRACTION13chain 'B' and (resid 396 through 458 )

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