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- PDB-6vi7: Probing extradiol dioxygenase mechanism in NAD(+) biosynthesis by... -

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Basic information

Entry
Database: PDB / ID: 6vi7
TitleProbing extradiol dioxygenase mechanism in NAD(+) biosynthesis by viewing reaction cycle intermediates - a substrate bidentately 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 / 'de novo' NAD+ biosynthetic process from L-tryptophan / quinolinate biosynthetic process / L-tryptophan catabolic process / ferrous iron binding
Similarity search - Function
3-hydroxyanthranilic acid dioxygenase / 3-hydroxyanthranilic acid dioxygenase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
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: 2.617 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 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Aug 12, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 2023Group: 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

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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
Water1,35175
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_775-y+2,-x+2,-z+1/61
Buried area5130 Å2
ΔGint-47 kcal/mol
Surface area15330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.040, 58.040, 231.580
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-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
#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-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.: 75 / 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: 2.45 Å3/Da / Density % sol: 49.8 %
Crystal growTemperature: 293 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 PILATUS 6M-F / 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: 2.61→50 Å / Num. obs: 7721 / % possible obs: 99.7 % / Redundancy: 25.5 % / Biso Wilson estimate: 22.04 Å2 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.045 / Rrim(I) all: 0.226 / Χ2: 1.365 / Net I/σ(I): 4.3 / Num. measured all: 196633
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.61-2.6626.31.2243740.9840.2411.2480.756100
2.66-2.727.10.8473540.9780.1650.8631.395100
2.7-2.7627.10.8363850.9930.1630.8530.656100
2.76-2.8126.70.5993630.9930.1170.6110.698100
2.81-2.8727.10.5893750.9930.1140.60.71100
2.87-2.9426.60.6053760.9880.1190.6170.724100
2.94-3.01270.4913670.9920.0960.50.819100
3.01-3.0926.70.3923640.9950.0770.40.929100
3.09-3.1926.70.3363800.9960.0660.3421.06100
3.19-3.2926.20.2993760.9940.0590.3051.199100
3.29-3.4126.50.2823950.9930.0560.2881.385100
3.41-3.5425.80.2833630.9970.0570.2892.159100
3.54-3.725.60.2523870.9950.0510.2571.88599.7
3.7-3.925.30.2213860.9990.0460.2262.057100
3.9-4.1425.20.2033980.9970.0420.2072.122100
4.14-4.4624.80.1743830.9960.0360.1782.159100
4.46-4.9123.90.1673930.9960.0350.1712.223100
4.91-5.6224.30.164110.9950.0320.1631.855100
5.62-7.0823.50.1364200.9980.0280.1391.515100
7.08-5019.20.1064710.9880.0250.1091.15195.3

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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: 2.617→37.955 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.59
RfactorNum. reflection% reflection
Rfree0.2895 693 10 %
Rwork0.1987 --
obs0.2077 6930 90.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.21 Å2 / Biso mean: 21.9238 Å2 / Biso min: 1.6 Å2
Refinement stepCycle: final / Resolution: 2.617→37.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1396 0 21 75 1492
Biso mean--29.04 18.61 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141468
X-RAY DIFFRACTIONf_angle_d1.291991
X-RAY DIFFRACTIONf_chiral_restr0.055196
X-RAY DIFFRACTIONf_plane_restr0.008267
X-RAY DIFFRACTIONf_dihedral_angle_d19.433849
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6173-2.81930.3521760.260268152
2.8193-3.10290.34671470.25751326100
3.1029-3.55160.3241510.21371355100
3.5516-4.47350.29261530.1698138099
4.4735-37.9550.21731660.1703149599

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