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

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Basic information

Entry
Database: PDB / ID: 6via
TitleObserving a ring-cleaving dioxygenase in action through a crystalline lens - a seven-membered lactone 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-EAY / : / : / HYDROXIDE ION / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.591 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 2.0Aug 5, 2020Group: Atomic model / Category: atom_site / Item: _atom_site.occupancy
Revision 2.1Oct 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 2.2Oct 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)23,1327
Polymers22,5901
Non-polymers5426
Water3,117173
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)46,26514
Polymers45,1812
Non-polymers1,08412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area5290 Å2
ΔGint-61 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.517, 58.517, 231.902
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 6 types, 179 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EAY / (2R,3E)-2-hydroxy-3-imino-2,3-dihydrooxepine-4-carboxylic acid


Mass: 169.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Nonpolymer detailsLigand EAY is an intermediate. This intermediate is thought to be a epsylon-lactone radical (on C11) ...Ligand EAY is an intermediate. This intermediate is thought to be a epsylon-lactone radical (on C11) with an Fe(III)-bound hydroxide or its resonance structure composed by a neutral epsylon-lactone (C11 and O12 form double bond) with an Fe(II)-bound hydroxide

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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: 51.51 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% 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-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 11, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.59→50 Å / Num. obs: 32318 / % possible obs: 98.2 % / Redundancy: 31.2 % / Biso Wilson estimate: 25.63 Å2 / Rmerge(I) obs: 0.083 / Χ2: 0.991 / Net I/σ(I): 5.9 / Num. measured all: 1009118
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.59-1.6233.10.82116000.3281100
1.62-1.6534.70.75515820.329199.9
1.65-1.6834.90.6916100.3451100
1.68-1.7134.20.57515980.371100
1.71-1.7533.60.48616000.5421100
1.75-1.7932.60.36615920.4231100
1.79-1.8430.40.32216280.4561100
1.84-1.8934.70.31616200.7611100
1.89-1.9431.30.34115921.4391100
1.94-2340.22216140.907199.9
2-2.07320.22816301.3561100
2.07-2.1631.40.14916320.9811100
2.16-2.2625.70.15116341.359199.6
2.26-2.3832.40.1116091.138199.8
2.38-2.5233.40.09716601.226199.9
2.52-2.7231.80.09316551.547199.9
2.72-2.9930.10.07616721.67199.7
2.99-3.43280.06516071.854194.5
3.43-4.32180.05913492.112177.8
4.32-5026.90.04618341.684195.2

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Processing

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

1yfu


Resolution: 1.591→30.732 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1982 6.19 %
Rwork0.2044 30035 -
obs0.2071 32017 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.68 Å2 / Biso mean: 41.9275 Å2 / Biso min: 20.24 Å2
Refinement stepCycle: final / Resolution: 1.591→30.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 31 173 1634
Biso mean--50.72 52.3 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141520
X-RAY DIFFRACTIONf_angle_d1.3342061
X-RAY DIFFRACTIONf_chiral_restr0.084203
X-RAY DIFFRACTIONf_plane_restr0.01274
X-RAY DIFFRACTIONf_dihedral_angle_d16.083883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.591-1.63060.30881380.2744212099
1.6306-1.67470.28021400.254211899
1.6747-1.7240.27631410.2406213199
1.724-1.77960.25311410.21832125100
1.7796-1.84320.25221430.20962150100
1.8432-1.9170.38911400.312211999
1.917-2.00420.32821360.2644207796
2.0042-2.10990.31481440.2382176100
2.1099-2.2420.26771430.21792180100
2.242-2.41510.28361440.23962175100
2.4151-2.6580.2761460.20612221100
2.658-3.04230.21161460.20122212100
3.0423-3.83190.24231370.1832206991
3.8319-30.7320.19691430.1713216288
Refinement TLS params.Method: refined / Origin x: -10.1576 Å / Origin y: -24.0878 Å / Origin z: 4.8173 Å
111213212223313233
T0.1998 Å2-0.0522 Å2-0.0016 Å2-0.2488 Å20.0107 Å2--0.1876 Å2
L1.1527 °2-0.3538 °20.2685 °2-1.9588 °2-1.5577 °2--4.0336 °2
S-0.1011 Å °0.2762 Å °0.0806 Å °-0.1421 Å °0.0026 Å °-0.0309 Å °-0.0268 Å °-0.1087 Å °0.1052 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 301
2X-RAY DIFFRACTION1allS1 - 231

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