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

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Basic information

Entry
Database: PDB / ID: 6foz
TitleThe crystal structure of P.fluorescens Kynurenine 3-monooxygenase (KMO) in complex with competitive inhibitor No. 13
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
5-(3,4-dichlorophenyl)furan-2-carboxylic acid / FLAVIN-ADENINE DINUCLEOTIDE / Kynurenine 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 8, 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
Revision 1.2May 1, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,3026
Polymers101,2172
Non-polymers2,0854
Water3,351186
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6513
Polymers50,6081
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6513
Polymers50,6081
Non-polymers1,0432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.540, 52.190, 136.210
Angle α, β, γ (deg.)90.000, 103.530, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAALAALA(chain 'A' and (resid 6 through 18 or resid 20...AA6 - 176 - 17
12LEULEUARGARG(chain 'A' and (resid 6 through 18 or resid 20...AA20 - 7120 - 71
13VALVALTYRTYR(chain 'A' and (resid 6 through 18 or resid 20...AA73 - 9773 - 97
14ASPASPARGARG(chain 'A' and (resid 6 through 18 or resid 20...AA100 - 110100 - 110
15ARGARGASNASN(chain 'A' and (resid 6 through 18 or resid 20...AA112 - 114112 - 114
16ILEILEARGARG(chain 'A' and (resid 6 through 18 or resid 20...AA116 - 141116 - 141
17ARGARGASPASP(chain 'A' and (resid 6 through 18 or resid 20...AA143 - 165143 - 165
18ASNASNLEULEU(chain 'A' and (resid 6 through 18 or resid 20...AA168 - 195168 - 195
19ILEILEPROPRO(chain 'A' and (resid 6 through 18 or resid 20...AA197 - 226197 - 226
110LEULEUPROPRO(chain 'A' and (resid 6 through 18 or resid 20...AA228 - 243228 - 243
111SERSERSERSER(chain 'A' and (resid 6 through 18 or resid 20...AA249 - 373249 - 373
112TYRTYRCYSCYS(chain 'A' and (resid 6 through 18 or resid 20...AA381 - 452381 - 452
213ALAALAALAALA(chain 'B' and (resid 6 through 18 or resid 20...BB6 - 176 - 17
214LEULEUARGARG(chain 'B' and (resid 6 through 18 or resid 20...BB20 - 7120 - 71
215VALVALTYRTYR(chain 'B' and (resid 6 through 18 or resid 20...BB73 - 9773 - 97
216ASPASPARGARG(chain 'B' and (resid 6 through 18 or resid 20...BB100 - 110100 - 110
217ARGARGASNASN(chain 'B' and (resid 6 through 18 or resid 20...BB112 - 114112 - 114
218ILEILEARGARG(chain 'B' and (resid 6 through 18 or resid 20...BB116 - 141116 - 141
219ARGARGASPASP(chain 'B' and (resid 6 through 18 or resid 20...BB143 - 165143 - 165
220ASNASNLEULEU(chain 'B' and (resid 6 through 18 or resid 20...BB168 - 195168 - 195
221ILEILEPROPRO(chain 'B' and (resid 6 through 18 or resid 20...BB197 - 226197 - 226
222LEULEUPROPRO(chain 'B' and (resid 6 through 18 or resid 20...BB228 - 243228 - 243
223SERSERSERSER(chain 'B' and (resid 6 through 18 or resid 20...BB249 - 373249 - 373
224TYRTYRCYSCYS(chain 'B' and (resid 6 through 18 or resid 20...BB381 - 452381 - 452

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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


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-E0H / 5-(3,4-dichlorophenyl)furan-2-carboxylic acid


Mass: 257.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H6Cl2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
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: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.15→66.89 Å / Num. obs: 51820 / % possible obs: 99.19 % / Redundancy: 3.2 % / Biso Wilson estimate: 37.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.06293 / Rpim(I) all: 0.04113 / Rrim(I) all: 0.07543 / Net I/σ(I): 12.94
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 5188 / CC1/2: 0.723 / Rpim(I) all: 0.3853 / % possible all: 99.81

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Processing

Software
NameVersionClassification
PHASER1.13_2998phasing
PHENIX1.13_2998refinement
xia2data reduction
xia2data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Inhouse

Resolution: 2.15→66.89 Å / SU ML: 0.2462 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0105
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 2467 4.76 %Random selection
Rwork0.1989 ---
obs0.2003 51799 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.38 Å2
Refinement stepCycle: LAST / Resolution: 2.15→66.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6797 0 138 186 7121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037183
X-RAY DIFFRACTIONf_angle_d0.62259786
X-RAY DIFFRACTIONf_chiral_restr0.04061074
X-RAY DIFFRACTIONf_plane_restr0.00351294
X-RAY DIFFRACTIONf_dihedral_angle_d15.2054266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.190.30871210.27462750X-RAY DIFFRACTION99.86
2.19-2.240.27731300.2752731X-RAY DIFFRACTION99.48
2.24-2.280.3291150.29982671X-RAY DIFFRACTION96.4
2.28-2.340.29831490.24432687X-RAY DIFFRACTION99.26
2.34-2.40.25391530.23912734X-RAY DIFFRACTION99.83
2.4-2.460.23861250.22732745X-RAY DIFFRACTION99.97
2.46-2.530.23431270.21972738X-RAY DIFFRACTION99.83
2.53-2.620.26981470.22112760X-RAY DIFFRACTION99.93
2.62-2.710.2751490.2232677X-RAY DIFFRACTION98.88
2.71-2.820.25851150.21422778X-RAY DIFFRACTION99.72
2.82-2.950.22921360.20372729X-RAY DIFFRACTION99.76
2.95-3.10.26151480.20442758X-RAY DIFFRACTION99.66
3.1-3.30.22931550.20032734X-RAY DIFFRACTION99.45
3.3-3.550.19071210.17982715X-RAY DIFFRACTION98.23
3.55-3.910.21370.1742722X-RAY DIFFRACTION97.78
3.91-4.470.19441370.16252746X-RAY DIFFRACTION98.87
4.47-5.630.20451570.17142772X-RAY DIFFRACTION99.36
5.63-66.920.22511450.20612885X-RAY DIFFRACTION99.34
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)
11.97661082198-0.9664627362-0.1695171122144.150048068821.461876450861.792760147930.01067778419620.3096548396340.0855634421835-0.159832659421-0.00584027747797-0.146151560356-0.0645775859273-0.0359362434613-0.004155763571230.262675713405-0.02800460174120.006363671628030.2654023837030.0517178907120.168282379932-41.956362813224.2415650148-197.421756221
22.24425925417-1.23841807055-0.04119770381763.68589464233-0.07078210512411.66720423682-0.09422263518530.0896112926229-0.1616637568820.231170360168-0.01639979326760.113863507593-0.01419140914940.08536932578140.09508080755780.206693489287-0.0455100527685-0.008877751864410.2560571248330.01181570246410.228283305205-43.22836418621.1612142863-191.554515984
32.67181855965-0.534596756604-0.606712357680.6818527370020.1963312428751.08972485603-0.0965897377344-0.208809094853-0.0845408829770.1956897333590.0685030051363-0.0563382993304-0.04693876020040.03113640600250.03548225659310.3234630036690.00552287208213-0.002719957726280.2274017814540.04361031491590.270004354764-47.384927624.2211449182-178.99253141
43.33973914057-1.693023687750.3936494351616.092582423590.1361410203632.73188841169-0.719541102771-0.5794745569270.309678050934-0.1584120274660.2675591697880.728495175649-1.7332723737-1.069314855660.3694787532621.332748429940.328958445081-0.2920974266510.8456818196920.05748879393170.642034195621-40.116892310246.0457095166-174.367379428
54.59397434348-0.4547932678880.7441562480694.081858597674.08159035775.84940041337-0.354184758876-1.097946813520.567967776952-0.2838076427030.141721431758-0.0144106323874-2.00151229896-0.2911603255160.2641430405471.187754617350.133893727654-0.1956369875340.651112755740.06319405665320.508613449738-34.720348204348.8009694385-166.678796465
61.58590322416-0.5127062249021.856475165124.80432321582-0.97714924622.449684805450.0485093742249-0.098439823167-0.1230735688340.0831959667385-0.00428260464716-0.0484021788283-0.003697127943-0.0535011073648-0.04722337311470.2035317921350.01307352016210.02029924265040.176354835758-0.009603663701650.196633876512-87.223714204-3.87506813661-133.14480988
72.490493060732.14196835031-0.987064490552.78088264668-0.9600113818631.923988613160.117213278006-0.02570033057810.04550756623440.19814849601-0.100274294329-0.00632624808959-0.2945862088190.00474328269914-0.06495307830350.2178134734220.0622227029680.007592559933860.261248627354-0.0109187432880.28434556222-82.87510108798.08743841452-139.167370032
82.895616651421.01963573308-0.8642137002561.65369645143-0.332797201070.972206735243-0.08116529055650.441997912405-0.275033287972-0.1848722142490.104091798647-0.115745482470.0617272333676-0.1715092665780.008561877784940.3077239176460.0292464997127-0.02303147575170.321361279231-0.05790858336020.280861224873-83.527056462-1.33837685937-149.880119937
91.52241261-0.07418220942591.625487501840.03907914661470.2954959457935.63163227686-0.9232582234150.007320298222270.3365144590190.808680670282-0.02132578029720.109301925786-1.914938288640.4497533242590.6643963114971.261564053890.17180767931-0.1286565789480.579554929880.09670162677480.662203988016-89.465003855422.0479642998-158.183077696
105.09331329635-2.666005799081.257529548263.795889483120.7052463466751.08529841045-0.2823033961240.6587046218860.5001577276410.5394728844580.05144631703080.0109558299569-1.64772154027-0.1779475610810.1161624952330.9640115223570.208824984001-0.1301288084720.5814571579570.1415142395390.452502920392-95.33507694724.2727001303-165.480306731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 169 )
3X-RAY DIFFRACTION3chain 'A' and (resid 170 through 372 )
4X-RAY DIFFRACTION4chain 'A' and (resid 373 through 412 )
5X-RAY DIFFRACTION5chain 'A' and (resid 413 through 455 )
6X-RAY DIFFRACTION6chain 'B' and (resid 7 through 57 )
7X-RAY DIFFRACTION7chain 'B' and (resid 58 through 138 )
8X-RAY DIFFRACTION8chain 'B' and (resid 139 through 371 )
9X-RAY DIFFRACTION9chain 'B' and (resid 372 through 412 )
10X-RAY DIFFRACTION10chain 'B' and (resid 413 through 452 )

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