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

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Basic information

Entry
Database: PDB / ID: 6vib
TitleObserving a ring-cleaving dioxygenase in action through a crystalline lens - enol tautomers of ACMS 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 / 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-2FO / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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)23,0095
Polymers22,5901
Non-polymers4194
Water2,954164
1
A: 3-hydroxyanthranilate 3,4-dioxygenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)46,01910
Polymers45,1812
Non-polymers8388
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area4170 Å2
ΔGint-25 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.330, 58.330, 232.040
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-448-

HOH

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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-2FO / (2Z,3Z)-2-[(2Z)-3-hydroxyprop-2-en-1-ylidene]-3-iminobutanedioic acid


Mass: 185.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7NO5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
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-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 S 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: 1.838→50 Å / Num. obs: 21430 / % possible obs: 99.6 % / Redundancy: 36.8 % / Biso Wilson estimate: 27.23 Å2 / Rmerge(I) obs: 0.143 / Χ2: 1.032 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.84-1.8737.80.93510380.5441100
1.87-1.9138.80.88110200.5511100
1.91-1.9438.90.72710620.5831100
1.94-1.9838.90.61310390.6061100
1.98-2.0338.50.5410390.6371100
2.03-2.0738.30.44310340.6661100
2.07-2.1237.50.38310500.731100
2.12-2.1834.80.31810450.7951100
2.18-2.2537.60.28810730.8061100
2.25-2.3239.50.25710350.879199.9
2.32-2.438.80.23510540.9111100
2.4-2.538.90.21610601.0061100
2.5-2.6138.40.19310751.0841100
2.61-2.7536.90.17510701.1981100
2.75-2.9235.10.16510911.3421100
2.92-3.1538.90.15510671.471199.9
3.15-3.4636.80.14810901.767199
3.46-3.9633.10.14311101.852199
3.96-4.9929.10.13111051.844196.2
4.99-5031.30.11712731.59199.4

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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: 1.84→42.294 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 2000 9.37 %
Rwork0.1966 19334 -
obs0.2012 21334 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.96 Å2 / Biso mean: 32.6058 Å2 / Biso min: 14.27 Å2
Refinement stepCycle: final / Resolution: 1.84→42.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1419 0 28 164 1611
Biso mean--32.59 39.42 -
Num. residues----175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021532
X-RAY DIFFRACTIONf_angle_d1.682087
X-RAY DIFFRACTIONf_chiral_restr0.098207
X-RAY DIFFRACTIONf_plane_restr0.011286
X-RAY DIFFRACTIONf_dihedral_angle_d19.417899
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.84-1.88390.30671370.2583132398
1.8839-1.93480.291370.23431332100
1.9348-1.99180.30961400.22481341100
1.9918-2.0560.25681390.23071343100
2.056-2.12950.28281390.22341358100
2.1295-2.21480.28851410.21511364100
2.2148-2.31560.2971420.21531359100
2.3156-2.43760.25811420.22141380100
2.4376-2.59040.25991410.21211361100
2.5904-2.79030.24541450.21921396100
2.7903-3.0710.2931450.2271404100
3.071-3.51520.23641450.1953139699
3.5152-4.42810.22531460.1617141998
4.4281-42.2940.19971610.1683155899

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