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- PDB-6vi8: Observing a ring-cleaving dioxygenase in action through a crystal... -

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Basic information

Entry
Database: PDB / ID: 6vi8
TitleObserving a ring-cleaving dioxygenase in action through a crystalline lens - a superoxo 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 / : / : / OXYGEN ATOM / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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)23,0097
Polymers22,5901
Non-polymers4196
Water3,261181
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)46,01914
Polymers45,1812
Non-polymers83812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6310 Å2
ΔGint-31 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.040, 58.040, 231.290
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-457-

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, 187 molecules

#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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.946→50 Å / Num. obs: 17991 / % possible obs: 99.9 % / Redundancy: 20.3 % / Biso Wilson estimate: 18.12 Å2 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.02 / Rrim(I) all: 0.092 / Χ2: 0.993 / Net I/σ(I): 7.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.9821.20.9418530.9640.2060.9640.829100
1.98-2.0220.90.8158770.9670.180.8350.853100
2.02-2.0621.10.6778680.9760.1490.6940.879100
2.06-2.120.80.5868750.9790.130.60.908100
2.1-2.1521.20.4998690.9830.1090.5110.908100
2.15-2.220.80.4218670.990.0930.4310.93100
2.2-2.2520.90.3748850.9920.0830.3830.954100
2.25-2.3120.90.3278790.9990.0730.3350.94100
2.31-2.3820.90.3038690.9960.0670.310.94100
2.38-2.4620.80.2578880.9980.0570.2630.942100
2.46-2.5420.80.2168840.9980.0480.2210.984100
2.54-2.6520.60.1879060.9970.0420.1910.993100
2.65-2.7720.70.1448790.9980.0320.1471.035100
2.77-2.9120.40.1199030.9980.0270.1221.051100
2.91-3.120.60.0958900.9990.0210.0981.088100
3.1-3.3320.10.0669140.9990.0150.0681.188100
3.33-3.6719.90.0539300.9990.0120.0541.197100
3.67-4.219.60.04493810.010.0451.1100
4.2-5.2919.20.03696110.0080.0371.011100
5.29-5016.50.03910560.9990.010.041.12497.7

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Processing

Software
NameVersionClassification
PHENIX1. 10refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YFU

1yfu


Resolution: 1.95→29.02 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.62
RfactorNum. reflection% reflection
Rfree0.2626 1790 10 %
Rwork0.2084 --
obs0.2138 17907 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.01 Å2 / Biso mean: 21.989 Å2 / Biso min: 4.85 Å2
Refinement stepCycle: final / Resolution: 1.95→29.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1430 0 23 181 1634
Biso mean--23.85 27.93 -
Num. residues----176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081513
X-RAY DIFFRACTIONf_angle_d1.032052
X-RAY DIFFRACTIONf_chiral_restr0.059202
X-RAY DIFFRACTIONf_plane_restr0.008275
X-RAY DIFFRACTIONf_dihedral_angle_d17.6880
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.95-1.99890.30311320.2612119599
1.9989-2.05770.27431320.24571191100
2.0577-2.12410.33191330.23251196100
2.1241-2.20.3211340.23641208100
2.2-2.28810.31191360.24041218100
2.2881-2.39220.28541350.24471219100
2.3922-2.51820.31181370.24241236100
2.5182-2.67590.32631340.22811198100
2.6759-2.88230.33341380.23221249100
2.8823-3.17210.2661380.21141234100
3.1721-3.63030.23551420.18541279100
3.6303-4.5710.1991420.15731283100
4.571-29.020.20081570.18571411100

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