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- PDB-6vi9: Observing a ring-cleaving dioxygenase in action through a crystal... -

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Basic information

Entry
Database: PDB / ID: 6vi9
TitleObserving a ring-cleaving dioxygenase in action through a crystalline lens - an alkylperoxo bound structure
Components3-hydroxyanthranilate 3,4-dioxygenase
KeywordsOXIDOREDUCTASE / In crystallo reaction / Extradiol dioxygenase / NAD+ biosynthesis / Intermediate
Function / homology
Function and homology information


3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate 3,4-dioxygenase activity / anthranilate metabolic process / quinolinate biosynthetic process / L-tryptophan catabolic process / NAD+ biosynthetic process / ferrous iron binding
Similarity search - Function
3-hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilic acid dioxygenase / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / Chem-QXM / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsWang, Y. / Liu, F. / Yang, Y. / Liu, A.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM108988 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R21MH107985 United States
National Science Foundation (NSF, United States)CHE-1623856 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107529 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens.
Authors: Wang, Y. / Liu, K.F. / Yang, Y. / Davis, I. / Liu, A.
History
DepositionJan 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0064
Polymers22,5901
Non-polymers4163
Water1,74797
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0138
Polymers45,1812
Non-polymers8326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area4000 Å2
ΔGint-26 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.790, 57.790, 231.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 3-hydroxyanthranilate 3,4-dioxygenase / 3-hydroxyanthranilate oxygenase / 3-HAO / 3-hydroxyanthranilic acid dioxygenase / HAD


Mass: 22590.377 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (strain ATCC 43123 / DSM 2839 / NBRC 102507 / CH34) (bacteria)
Strain: ATCC 43123 / DSM 2839 / NBRC 102507 / CH34 / Gene: nbaC, Rmet_5193 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q1LCS4, 3-hydroxyanthranilate 3,4-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-QXM / (5R,6Z)-5-(hydroperoxy-kappaO)-5-(hydroxy-kappaO)-6-iminocyclohexa-1,3-diene-1-carboxylato(2-)iron


Mass: 237.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H4FeNO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 15% PEG8000, 0.1 M Tris-HCl, 0.2 M magnesium chloride, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 14, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 11036 / % possible obs: 99.6 % / Redundancy: 16.7 % / Biso Wilson estimate: 26.38 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 6
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.996 / Num. unique obs: 478 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YFU

1yfu


Resolution: 2.31→30.55 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.71
RfactorNum. reflection% reflection
Rfree0.275 992 10 %
Rwork0.225 --
obs0.23 9921 90.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.83 Å2
Refinement stepCycle: LAST / Resolution: 2.31→30.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 23 98 1509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161456
X-RAY DIFFRACTIONf_angle_d1.0211981
X-RAY DIFFRACTIONf_dihedral_angle_d3.967853
X-RAY DIFFRACTIONf_chiral_restr0.054197
X-RAY DIFFRACTIONf_plane_restr0.007264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.4260.3871530.2839478X-RAY DIFFRACTION35
2.426-2.57790.33061490.27791343X-RAY DIFFRACTION100
2.5779-2.77690.3411540.27441380X-RAY DIFFRACTION100
2.7769-3.05610.30611520.28171373X-RAY DIFFRACTION100
3.0561-3.49780.3071550.22571386X-RAY DIFFRACTION100
3.4978-4.40470.2371590.18721432X-RAY DIFFRACTION100
4.4047-30.550.22231700.19361537X-RAY DIFFRACTION99

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