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- PDB-6fph: The crystal structure of P.fluorescens Kynurenine 3-monooxygenase... -

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Basic information

Entry
Database: PDB / ID: 6fph
TitleThe crystal structure of P.fluorescens Kynurenine 3-monooxygenase (KMO) in complex with competitive inhibitor No. 1h
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / Inhibitor
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
Chem-E1W / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLevy, C.W. / Leys, D.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/P009042/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/R000093/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/J020192/1 United Kingdom
Medical Research Council (United Kingdom)MR/N00373X/1 United Kingdom
CitationJournal: Commun Biol / Year: 2019
Title: A brain-permeable inhibitor of the neurodegenerative disease target kynurenine 3-monooxygenase prevents accumulation of neurotoxic metabolites.
Authors: Zhang, S. / Sakuma, M. / Deora, G.S. / Levy, C.W. / Klausing, A. / Breda, C. / Read, K.D. / Edlin, C.D. / Ross, B.P. / Wright Muelas, M. / Day, P.J. / O'Hagan, S. / Kell, D.B. / Schwarcz, R. ...Authors: Zhang, S. / Sakuma, M. / Deora, G.S. / Levy, C.W. / Klausing, A. / Breda, C. / Read, K.D. / Edlin, C.D. / Ross, B.P. / Wright Muelas, M. / Day, P.J. / O'Hagan, S. / Kell, D.B. / Schwarcz, R. / Leys, D. / Heyes, D.J. / Giorgini, F. / Scrutton, N.S.
History
DepositionFeb 9, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kynurenine 3-monooxygenase
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4468
Polymers101,2172
Non-polymers2,2296
Water8,413467
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7234
Polymers50,6081
Non-polymers1,1153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7234
Polymers50,6081
Non-polymers1,1153
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.351, 53.253, 135.844
Angle α, β, γ (deg.)90.000, 103.812, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
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: 50608.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: kmo, qbsG / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / References: UniProt: Q84HF5, kynurenine 3-monooxygenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-E1W / 6-chloranyl-5,7-dimethyl-4-(1~{H}-1,2,3,4-tetrazol-5-ylmethyl)-1,4-benzoxazin-3-one


Mass: 293.709 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH6.5, 18 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→49.39 Å / Num. obs: 66361 / % possible obs: 99.72 % / Redundancy: 3.4 % / Biso Wilson estimate: 27.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05622 / Rpim(I) all: 0.03601 / Net I/σ(I): 13.72
Reflection shellResolution: 2→2.071 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.5078 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.833 / Rpim(I) all: 0.3209 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Inhouse

Resolution: 2→29.35 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.8782
RfactorNum. reflection% reflectionSelection details
Rfree0.2184 3248 4.9 %Random selection
Rwork0.1915 ---
obs0.1928 66342 99.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.79 Å2
Refinement stepCycle: LAST / Resolution: 2→29.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6843 0 148 467 7458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00237247
X-RAY DIFFRACTIONf_angle_d0.5529875
X-RAY DIFFRACTIONf_chiral_restr0.03891082
X-RAY DIFFRACTIONf_plane_restr0.0031301
X-RAY DIFFRACTIONf_dihedral_angle_d16.96264320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.2861140.24072749X-RAY DIFFRACTION100
2.03-2.060.26281460.23122738X-RAY DIFFRACTION99.97
2.06-2.10.28111560.23572692X-RAY DIFFRACTION99.79
2.1-2.130.24131560.23432754X-RAY DIFFRACTION99.86
2.13-2.170.23951380.21312669X-RAY DIFFRACTION99.96
2.17-2.210.25971610.21552739X-RAY DIFFRACTION99.86
2.21-2.260.23211620.21432680X-RAY DIFFRACTION99.89
2.26-2.310.26841440.21022725X-RAY DIFFRACTION100
2.31-2.360.23161390.20772734X-RAY DIFFRACTION99.93
2.36-2.420.22941430.20642759X-RAY DIFFRACTION99.97
2.42-2.480.21541310.20122687X-RAY DIFFRACTION99.82
2.48-2.560.2151270.20012768X-RAY DIFFRACTION99.72
2.56-2.640.23991460.20512731X-RAY DIFFRACTION99.83
2.64-2.730.23511160.20512761X-RAY DIFFRACTION99.86
2.73-2.840.23151440.19652760X-RAY DIFFRACTION99.93
2.84-2.970.23031550.1932722X-RAY DIFFRACTION99.86
2.97-3.130.21721570.20492730X-RAY DIFFRACTION99.83
3.13-3.320.23991150.2062785X-RAY DIFFRACTION99.86
3.32-3.580.22471180.18492762X-RAY DIFFRACTION99.38
3.58-3.940.19931570.1682723X-RAY DIFFRACTION99.38
3.94-4.510.18931540.15632755X-RAY DIFFRACTION99.52
4.51-5.670.16981420.1552780X-RAY DIFFRACTION99.42
5.67-29.350.20491270.19212891X-RAY DIFFRACTION99.08

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