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- PDB-8uiq: H47Q NicC with 2-mercaptopyridine ligand -

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Basic information

Entry
Database: PDB / ID: 8uiq
TitleH47Q NicC with 2-mercaptopyridine ligand
Components6-hydroxynicotinate 3-monooxygenase
KeywordsOXIDOREDUCTASE / ligand bound
Function / homology
Function and homology information


6-hydroxynicotinate 3-monooxygenase / 6-hydroxynicotinate 3-monooxygenase activity / nicotinate catabolic process / FAD binding / monooxygenase activity
Similarity search - Function
: / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2-PYRIDINETHIOL / 6-hydroxynicotinate 3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida KT2440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHicks, K.A. / Perry, K. / Turlington, Z.R. / Vaz Ferreira de Macedo, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1817633 United States
CitationJournal: Arch.Biochem.Biophys. / Year: 2024
Title: Ligand bound structure of a 6-hydroxynicotinic acid 3-monooxygenase provides mechanistic insights.
Authors: Turlington, Z.R. / Vaz Ferreira de Macedo, S. / Perry, K. / Belsky, S.L. / Faust, J.A. / Snider, M.J. / Hicks, K.A.
History
DepositionOct 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 6-hydroxynicotinate 3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3173
Polymers45,4201
Non-polymers8972
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.376, 69.244, 115.270
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein 6-hydroxynicotinate 3-monooxygenase


Mass: 45420.066 Da / Num. of mol.: 1 / Mutation: H47Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) / Gene: nicC / Production host: Escherichia coli (E. coli) / References: UniProt: Q88FY2
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-PYS / 2-PYRIDINETHIOL


Mass: 111.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5NS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, pH 7.5, 15-25% polyethylene glycol (PEG) 3350, and 0.2 M magnesium chloride hexahydrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11831N
21831N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.97918
SYNCHROTRONAPS 24-ID-C21.7712
Detector
TypeIDDetectorDate
DECTRIS EIGER2 X 16M1PIXELApr 11, 2023
DECTRIS EIGER2 X 16M2PIXELApr 11, 2023
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
21.77121
Reflection

Entry-ID: 8UIQ / CC1/2: 0.997

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)Rmerge(I) obsDiffraction-IDNet I/σ(I)
2.17-59.362048098.566.8350.196417.66
2.431-44.411410994.4224.70.4798214.88
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-IDRmerge(I) obs
2.17-2.24819910.7241
2.431-2.51811990.91721.01

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.17→59.36 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 0.46 / Phase error: 35.6149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2829 1893 4.97 %
Rwork0.245 36232 -
obs0.2469 20468 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.7 Å2
Refinement stepCycle: LAST / Resolution: 2.17→59.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2837 0 60 115 3012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022971
X-RAY DIFFRACTIONf_angle_d0.48784049
X-RAY DIFFRACTIONf_chiral_restr0.0397435
X-RAY DIFFRACTIONf_plane_restr0.0032523
X-RAY DIFFRACTIONf_dihedral_angle_d10.7912410
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.17-2.220.41441350.40292576X-RAY DIFFRACTION98.33
2.22-2.280.40851190.3712614X-RAY DIFFRACTION99.06
2.28-2.350.35351380.35592578X-RAY DIFFRACTION98.51
2.35-2.430.39291510.33232558X-RAY DIFFRACTION98.69
2.43-2.510.31851280.32222625X-RAY DIFFRACTION98.46
2.51-2.610.32951500.2982627X-RAY DIFFRACTION98.79
2.62-2.730.35671360.29092572X-RAY DIFFRACTION98.98
2.73-2.880.32561560.2732562X-RAY DIFFRACTION98.62
2.88-3.060.35111370.27612549X-RAY DIFFRACTION97.07
3.06-3.290.26391340.24442544X-RAY DIFFRACTION96.75
3.29-3.630.23951260.22072654X-RAY DIFFRACTION99.57
3.63-4.150.22371320.18572614X-RAY DIFFRACTION99.64
4.15-5.230.22951310.1852630X-RAY DIFFRACTION99.46
5.23-59.360.241200.20522529X-RAY DIFFRACTION96.08

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