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- PDB-5y7a: Crystal structure of Pseudomonas fluorescens Kynurenine 3-monooxy... -

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Basic information

Entry
Database: PDB / ID: 5y7a
TitleCrystal structure of Pseudomonas fluorescens Kynurenine 3-monooxygenase in complex with L-KYN
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / enzyme / L-kynurenine (L-Kyn) / 3-hydroxy-L-kynurenine (L-3OHKyn) / KMO / Ro61-8048
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 / MOLECULAR REPLACEMENT / Resolution: 1.846 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 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1073
Polymers52,1131
Non-polymers9942
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-7 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.480, 46.513, 71.311
Angle α, β, γ (deg.)90.00, 104.34, 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: 52113.070 Da / Num. of mol.: 1
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.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C10H12N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 6.5
Details: 0.1 M Bis-Tris at pH 6.5, 18% w/v PEG3350, and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.846→50 Å / Num. obs: 36572 / % possible obs: 97.6 % / Redundancy: 3.8 % / Net I/σ(I): 33.2

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y77

5y77


Resolution: 1.846→38.584 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.64
RfactorNum. reflection% reflection
Rfree0.2174 1829 5 %
Rwork0.1736 --
obs0.1759 36557 96.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.846→38.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3491 0 68 370 3929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063704
X-RAY DIFFRACTIONf_angle_d1.3355053
X-RAY DIFFRACTIONf_dihedral_angle_d14.9451388
X-RAY DIFFRACTIONf_chiral_restr0.082560
X-RAY DIFFRACTIONf_plane_restr0.004668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8463-1.89620.25751170.20382442X-RAY DIFFRACTION89
1.8962-1.9520.21251380.19282664X-RAY DIFFRACTION97
1.952-2.0150.22951250.18932652X-RAY DIFFRACTION97
2.015-2.08710.23921430.18112650X-RAY DIFFRACTION97
2.0871-2.17060.23731440.18152663X-RAY DIFFRACTION97
2.1706-2.26940.21421420.18122650X-RAY DIFFRACTION97
2.2694-2.3890.26911500.18572678X-RAY DIFFRACTION98
2.389-2.53870.24621300.18222711X-RAY DIFFRACTION98
2.5387-2.73460.24061570.18652702X-RAY DIFFRACTION98
2.7346-3.00970.20911490.18332676X-RAY DIFFRACTION98
3.0097-3.4450.23111400.17142741X-RAY DIFFRACTION98
3.445-4.33940.18761480.14452721X-RAY DIFFRACTION98
4.3394-38.59230.19211460.17122778X-RAY DIFFRACTION97
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)
11.3819-0.58291.47643.6751-0.50152.0659-0.00230.14710.1705-0.06830.05320.055-0.113-0.0965-0.02690.0979-0.0008-0.01080.10930.00550.12121.85526.036149.8114
24.8613-1.6403-2.311.68220.86582.6696-0.0140.1235-0.4452-0.0677-0.14980.07080.26880.21370.12120.15560.0261-0.02390.1545-0.02480.148532.4228-9.770444.969
31.1335-0.6468-0.65251.04530.76652.09720.0247-0.03570.2027-0.08630.0949-0.1201-0.32360.1533-0.09840.1645-0.0468-0.00290.11980.00790.18334.2858.453949.051
40.693-0.2717-0.46630.54410.32672.12880.0146-0.06840.048-0.0490.0956-0.1303-0.13370.5463-0.10130.1531-0.0459-0.02130.2267-0.04340.173542.21093.291650.7858
54.3342-3.38171.76294.2987-0.91053.06720.22210.33830.0898-0.1798-0.1026-0.22590.43870.0274-0.09590.3125-0.051-0.04510.19420.00190.184750.0439-19.58961.4095
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 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 373 )
5X-RAY DIFFRACTION5chain 'A' and (resid 374 through 457 )

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