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- PDB-5fn0: Crystal structure of Pseudomonas fluorescens kynurenine-3- monoox... -

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Basic information

Entry
Database: PDB / ID: 5fn0
TitleCrystal structure of Pseudomonas fluorescens kynurenine-3- monooxygenase (KMO) in complex with GSK180
ComponentsKYNURENINE 3-MONOOXYGENASE
KeywordsOXIDOREDUCTASE / KMO
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 / Chem-JHY / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.19 Å
AuthorsMole, D.J. / Webster, S.P. / Uings, I. / Zheng, X. / Binnie, M. / Wilson, K. / Hutchinson, J.P. / Mirguet, O. / Walker, A. / Beaufils, B. ...Mole, D.J. / Webster, S.P. / Uings, I. / Zheng, X. / Binnie, M. / Wilson, K. / Hutchinson, J.P. / Mirguet, O. / Walker, A. / Beaufils, B. / Ancellin, N. / Trottet, L. / Beneton, V. / Mowat, C.G. / Wilkinson, M. / Rowland, P. / Haslam, C. / McBride, A. / Homer, N.Z.M. / Baily, J.E. / Sharp, M.G.F. / Garden, O.J. / Hughes, J. / Howie, S.E.M. / Holmes, D. / Liddle, J. / Iredale, J.P.
CitationJournal: Nat.Med. (N.Y.) / Year: 2016
Title: Kynurenine-3-Monooxygenase Inhibition Prevents Multiple Organ Failure in Rodent Models of Acute Pancreatitis.
Authors: Mole, D.J. / Webster, S.P. / Uings, I. / Zheng, X. / Binnie, M. / Wilson, K. / Hutchinson, J.P. / Mirguet, O. / Walker, A. / Beaufils, B. / Ancellin, N. / Trottet, L. / Beneton, V. / Mowat, ...Authors: Mole, D.J. / Webster, S.P. / Uings, I. / Zheng, X. / Binnie, M. / Wilson, K. / Hutchinson, J.P. / Mirguet, O. / Walker, A. / Beaufils, B. / Ancellin, N. / Trottet, L. / Beneton, V. / Mowat, C.G. / Wilkinson, M. / Rowland, P. / Haslam, C. / Mcbride, A. / Homer, N.Z. / Baily, J.E. / Sharp, M.G. / Garden, O.J. / Hughes, J. / Howie, S.E. / Holmes, D.S. / Liddle, J. / Iredale, J.P.
History
DepositionNov 10, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: KYNURENINE 3-MONOOXYGENASE
D: KYNURENINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,20512
Polymers202,9584
Non-polymers4,2468
Water5,368298
1
A: KYNURENINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8013
Polymers50,7401
Non-polymers1,0622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KYNURENINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8013
Polymers50,7401
Non-polymers1,0622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: KYNURENINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8013
Polymers50,7401
Non-polymers1,0622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: KYNURENINE 3-MONOOXYGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8013
Polymers50,7401
Non-polymers1,0622
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)186.850, 105.290, 133.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
KYNURENINE 3-MONOOXYGENASE / PFKMO / KYNURENINE 3-HYDROXYLASE


Mass: 50739.520 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-JHY / 3-(5,6-DICHLORO-2-OXOBENZO[D]OXAZOL-3(2H)-YL)PROPANOIC ACID


Mass: 276.073 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H7Cl2NO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3.24 Å3/Da / Density % sol: 62.02 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: HANGING DROP VAPOUR DIFFUSION. 0.1M HEPES PH 7.0, 10% GLYCEROL, 10% 2-PROPANOL, 6.5% PEG 4000, 10MM KCL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97924
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 3.19→187 Å / Num. obs: 44508 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 111.17 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.4
Reflection shellResolution: 3.19→3.21 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.19→93.43 Å / Cor.coef. Fo:Fc: 0.9503 / Cor.coef. Fo:Fc free: 0.9329 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.354
RfactorNum. reflection% reflectionSelection details
Rfree0.1964 2244 5.05 %RANDOM
Rwork0.1569 ---
obs0.1589 44463 99.59 %-
Displacement parametersBiso mean: 113.61 Å2
Baniso -1Baniso -2Baniso -3
1--4.9094 Å20 Å20 Å2
2---8.1692 Å20 Å2
3---13.0786 Å2
Refine analyzeLuzzati coordinate error obs: 0.695 Å
Refinement stepCycle: LAST / Resolution: 3.19→93.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14092 0 280 298 14670
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114704HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1220024HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5056SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes368HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2384HARMONIC5
X-RAY DIFFRACTIONt_it14704HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion21.03
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1876SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact16975SEMIHARMONIC4
LS refinement shellResolution: 3.19→3.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2736 157 5.1 %
Rwork0.2016 2923 -
all0.2053 3080 -
obs--99.59 %
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)
12.0051-0.38160.42142.0321-0.75612.9578-0.3582-0.55580.60490.19750.2023-0.4193-1.08850.420.1560.14810.1408-0.1375-0.324-0.2196-0.2104-33.551147.5058-34.8867
21.9571-0.2147-0.30681.8038-0.02454.634-0.3693-0.6469-0.47950.21690.27870.12751.0885-0.73250.09070.07770.17060.1129-0.17470.1863-0.299-55.41758.7221-30.0174
32.6951-1.16971.081.6852-0.72212.41030.46160.56410.2965-0.6015-0.4815-0.554-0.22830.75650.0199-0.24490.3040.19290.05110.1435-0.2332-5.781318.204-38.5
43.0249-0.9742-0.26812.37870.35344.12030.56890.6418-0.4791-0.5361-0.51960.78580.7368-0.912-0.0494-0.37070.1891-0.23070.0602-0.2627-0.1285-85.820534.9851-30.0529
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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