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- PDB-6x11: Observing a ring-cleaving dioxygenase in action through a crystal... -

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Basic information

Entry
Database: PDB / ID: 6x11
TitleObserving a ring-cleaving dioxygenase in action through a crystalline lens - an enol tautomer of ACMS 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
Chem-2FO / : / 3-hydroxyanthranilate 3,4-dioxygenase
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 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
DepositionMay 17, 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 18, 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
Water1,892105
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 area4560 Å2
ΔGint-54 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.626, 58.626, 231.814
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-399-

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)
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.: 105 / 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: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging 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: 22-BM / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.097→50 Å / Num. obs: 14606 / % possible obs: 98.5 % / Redundancy: 27.5 % / Biso Wilson estimate: 30.39 Å2 / Rmerge(I) obs: 0.107 / Χ2: 1.029 / Net I/σ(I): 7.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.1-2.1415.90.6496650.641196.4
2.14-2.1820.50.7347260.641100
2.18-2.2219.20.6477040.694199.3
2.22-2.2611.90.3626272.887185.5
2.26-2.3116.50.6296560.709194
2.31-2.3726.60.4747230.6831100
2.37-2.4225.70.3397190.669199.6
2.42-2.4927.50.3227140.6971100
2.49-2.5630.30.2957270.6951100
2.56-2.6532.60.2577190.7071100
2.65-2.7434.10.2157310.7351100
2.74-2.8534.30.1757260.7361100
2.85-2.9834.30.1617470.7951100
2.98-3.1434.40.1147300.8621100
3.14-3.3333.80.0897451.0121100
3.33-3.5931.90.087471.174199.9
3.59-3.9522.30.0927382.032196
3.95-4.5232.40.0787702.059199.9
4.52-5.731.90.067951.469199.7
5.7-5028.50.0438971.332199.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.1refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YFU

1yfu


Resolution: 2.097→38.189 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2793 1446 9.99 %
Rwork0.2189 13035 -
obs0.2249 14481 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.66 Å2 / Biso mean: 35.4492 Å2 / Biso min: 16.18 Å2
Refinement stepCycle: final / Resolution: 2.097→38.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1414 0 23 105 1542
Biso mean--38.83 38.64 -
Num. residues----174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141485
X-RAY DIFFRACTIONf_angle_d1.4142015
X-RAY DIFFRACTIONf_chiral_restr0.071199
X-RAY DIFFRACTIONf_plane_restr0.008269
X-RAY DIFFRACTIONf_dihedral_angle_d20.485865
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.097-2.17190.37061370.2773123297
2.1719-2.25890.46861290.401119192
2.2589-2.36170.3911370.2957123497
2.3617-2.48620.27781430.24051280100
2.4862-2.64190.30951450.23661302100
2.6419-2.84580.311450.23551307100
2.8458-3.13210.32661480.24441320100
3.1321-3.5850.25031480.21051337100
3.585-4.51560.23241470.1789133897
4.5156-38.1890.23151670.17511494100

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