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

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Basic information

Entry
Database: PDB / ID: 6fox
TitleThe crystal structure of P.fluorescens Kynurenine 3-monooxygenase (KMO) in complex with kynurenine
ComponentsKynurenine 3-monooxygenase
KeywordsOXIDOREDUCTASE / Substrate
Function / homology
Function and homology information


kynurenine 3-monooxygenase / kynurenine 3-monooxygenase activity / kynurenine metabolic process / anthranilate metabolic process / NAD(P)H oxidase H2O2-forming activity / quinolinate biosynthetic process / 'de novo' NAD+ biosynthetic process from L-tryptophan / L-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: 1.9 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
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
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)103,0366
Polymers101,2172
Non-polymers1,8194
Water14,358797
1
A: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4343
Polymers50,6081
Non-polymers8262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kynurenine 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6023
Polymers50,6081
Non-polymers9942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.908, 52.542, 136.173
Angle α, β, γ (deg.)90.000, 104.142, 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


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


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 797 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
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: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.899→44.02 Å / Num. obs: 74533 / % possible obs: 97.73 % / Redundancy: 4.1 % / Biso Wilson estimate: 19.56 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0617 / Rpim(I) all: 0.03467 / Net I/σ(I): 14.28
Reflection shellResolution: 1.899→1.967 Å / Redundancy: 4 % / Rmerge(I) obs: 0.1846 / Mean I/σ(I) obs: 5.43 / Num. unique obs: 7153 / CC1/2: 0.957 / Rpim(I) all: 0.1034 / % possible all: 94.67

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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: 1.9→44.02 Å / SU ML: 0.2401 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 23.9234
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 1961 2.63 %Random selection
Rwork0.1701 ---
obs0.1712 74439 97.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.97 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 122 802 7875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00437361
X-RAY DIFFRACTIONf_angle_d0.677210036
X-RAY DIFFRACTIONf_chiral_restr0.04331106
X-RAY DIFFRACTIONf_plane_restr0.0041330
X-RAY DIFFRACTIONf_dihedral_angle_d15.7334405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.39451350.33884952X-RAY DIFFRACTION93.31
1.95-20.23271370.20985116X-RAY DIFFRACTION97.99
2-2.060.25911400.18515149X-RAY DIFFRACTION98.6
2.06-2.120.2091380.17575209X-RAY DIFFRACTION98.73
2.12-2.20.21151440.16815217X-RAY DIFFRACTION99.06
2.2-2.290.27231220.20924937X-RAY DIFFRACTION93.58
2.29-2.390.21171470.17025239X-RAY DIFFRACTION99.43
2.39-2.520.18791450.16325231X-RAY DIFFRACTION99.33
2.52-2.680.21841380.17065241X-RAY DIFFRACTION99.43
2.68-2.880.24291460.16955252X-RAY DIFFRACTION99.28
2.88-3.170.2581420.17635230X-RAY DIFFRACTION98.26
3.17-3.630.19211430.15635187X-RAY DIFFRACTION97.8
3.63-4.580.15511400.13515150X-RAY DIFFRACTION96.06
4.58-44.030.19861440.15475368X-RAY DIFFRACTION97.63
Refinement TLS params.Method: refined / Origin x: 111.60026503 Å / Origin y: 6.67181144148 Å / Origin z: -98.1626173491 Å
111213212223313233
T0.128119592397 Å20.00396072483822 Å2-0.0114985462399 Å2-0.0972864730314 Å2-0.0129345173523 Å2--0.153195131172 Å2
L0.202349885564 °20.0943350781526 °2-0.221480709717 °2-0.0646358957385 °2-0.194209458696 °2--0.576039038039 °2
S-0.0243916972272 Å °0.00996631443661 Å °-0.011097153346 Å °-0.0458269226697 Å °0.018165261834 Å °-0.017325942323 Å °0.0302299200229 Å °0.036370259941 Å °0.0069917633238 Å °
Refinement TLS groupSelection details: all

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