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- PDB-6vi6: Observing a ring-cleaving dioxygenase in action through a crystal... -

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Basic information

Entry
Database: PDB / ID: 6vi6
TitleObserving a ring-cleaving dioxygenase in action through a crystalline lens - a substrate monodentately 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
3-HYDROXYANTHRANILIC ACID / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,9775
Polymers22,5901
Non-polymers3874
Water2,918162
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)45,95510
Polymers45,1812
Non-polymers7748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5100 Å2
ΔGint-41 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.990, 57.990, 231.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-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
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-3HA / 3-HYDROXYANTHRANILIC ACID / 2-AMINO-3-HYDROXYBENZOIC ACID


Mass: 153.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
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 S 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: 1.9→50 Å / Num. obs: 19246 / % possible obs: 99.7 % / Redundancy: 19 % / Biso Wilson estimate: 21.06 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.021 / Rrim(I) all: 0.088 / Χ2: 1.061 / Net I/σ(I): 6.9 / Num. measured all: 365092
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.9319.70.8969480.9810.2060.920.869100
1.93-1.9720.10.849140.9720.1910.8620.794100
1.97-2.01200.6679320.9820.1520.6850.814100
2.01-2.0519.90.5689350.9850.130.5820.827100
2.05-2.0919.70.4719420.990.1080.4830.947100
2.09-2.1420.10.4229350.9880.0960.4330.881100
2.14-2.1919.70.3299260.9940.0760.3380.918100
2.19-2.2519.60.2849370.9960.0650.2921.023100
2.25-2.3219.70.2749680.9960.0630.2810.997100
2.32-2.3919.50.2249370.9980.0520.230.976100
2.39-2.4819.50.199390.9970.0440.1951.006100
2.48-2.5819.30.1669580.9980.0390.1711.006100
2.58-2.719.20.1389470.9980.0320.1421.116100
2.7-2.8419.30.1129700.9980.0260.1151.15100
2.84-3.02190.0979680.9990.0230.0991.166100
3.02-3.2518.70.0759730.9980.0180.0771.324100
3.25-3.5818.40.0629810.9990.0150.0641.431100
3.58-4.0917.70.05410050.9990.0140.0561.389100
4.09-5.1616.20.04810200.9990.0120.051.27699.1
5.16-5015.20.0511110.9990.0130.0521.39295.5

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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: 1.901→28.995 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.44
RfactorNum. reflection% reflection
Rfree0.2543 1915 10 %
Rwork0.1985 --
obs0.204 19142 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.14 Å2 / Biso mean: 34.3174 Å2 / Biso min: 12.06 Å2
Refinement stepCycle: final / Resolution: 1.901→28.995 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1409 0 21 172 1602
Biso mean--37.17 44.35 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151479
X-RAY DIFFRACTIONf_angle_d1.412007
X-RAY DIFFRACTIONf_chiral_restr0.092199
X-RAY DIFFRACTIONf_plane_restr0.009269
X-RAY DIFFRACTIONf_dihedral_angle_d16.624861
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9014-1.9490.29281340.27051205100
1.949-2.00160.28341320.25211197100
2.0016-2.06050.30751320.23741185100
2.0605-2.1270.27941340.22971203100
2.127-2.2030.28391330.22691193100
2.203-2.29120.28221350.22211216100
2.2912-2.39540.25891340.221213100
2.3954-2.52160.30591370.21761222100
2.5216-2.67950.2951330.21271202100
2.6795-2.88620.25381380.20621240100
2.8862-3.17640.23531380.20191235100
3.1764-3.63520.22161390.17851264100
3.6352-4.57710.21041420.1572127299
4.5771-28.9950.25681540.1784138098
Refinement TLS params.Method: refined / Origin x: 9.3516 Å / Origin y: 23.5521 Å / Origin z: 4.4958 Å
111213212223313233
T0.1215 Å2-0.0653 Å20.0009 Å2-0.2905 Å2-0.0694 Å2--0.186 Å2
L1.081 °2-0.5441 °2-0.074 °2-0.989 °20.3019 °2--2.5672 °2
S-0.1631 Å °0.4549 Å °-0.1269 Å °-0.0599 Å °-0.0352 Å °0.0795 Å °0.1021 Å °0.1392 Å °0.1335 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 300
2X-RAY DIFFRACTION1allS1 - 180

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