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- PDB-7tcl: Crystal structure of P.IsnB complexed with tyrosine isonitrile -

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Basic information

Entry
Database: PDB / ID: 7tcl
TitleCrystal structure of P.IsnB complexed with tyrosine isonitrile
ComponentsTauD/TfdA family dioxygenase
KeywordsOXIDOREDUCTASE / TauD/TfdA family dioxygenase / vinyl isonitrile biosynthesis
Function / homologyTauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / dioxygenase activity / (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoic acid / : / TauD/TfdA family dioxygenase
Function and homology information
Biological speciesPhotorhabdus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKim, W. / Zhang, Y.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104896 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125882 United States
CitationJournal: Nat Commun / Year: 2022
Title: Elucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate.
Authors: Kim, W. / Chen, T.Y. / Cha, L. / Zhou, G. / Xing, K. / Canty, N.K. / Zhang, Y. / Chang, W.C.
History
DepositionDec 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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

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Assembly

Deposited unit
X: TauD/TfdA family dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5736
Polymers33,0391
Non-polymers5345
Water2,900161
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.868, 58.375, 102.589
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TauD/TfdA family dioxygenase


Mass: 33039.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus (bacteria) / Gene: GPY51_01460 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6L9JEC7
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-I3J / (2S)-3-(4-hydroxyphenyl)-2-isocyanopropanoic acid / tyrosine isonitrile


Mass: 191.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6.5, 0.2M Ammonium Sulfate, 30% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03314 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 21617 / % possible obs: 99.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.048 / Rrim(I) all: 0.124 / Χ2: 0.903 / Net I/σ(I): 4.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.0150.71310540.7020.3450.7950.55899.5
2.01-2.055.40.70710470.7110.3290.7830.64399.7
2.05-2.095.70.62910830.760.2830.6920.72299.5
2.09-2.135.90.56410380.7850.2480.6180.73399.8
2.13-2.1860.54710910.7870.2380.5990.80999.4
2.18-2.235.90.45410390.8720.20.4980.85299.3
2.23-2.295.50.41410650.8580.190.4580.97898.7
2.29-2.356.90.38110690.9230.1540.4120.89199.6
2.35-2.427.10.32810750.9330.130.3540.88499.8
2.42-2.497.10.28910670.950.1150.3120.87699.6
2.49-2.586.90.2510620.9660.1020.2710.8399.4
2.58-2.696.90.20710740.9660.0840.2240.88999.7
2.69-2.816.80.17710830.9790.0730.1920.91699.3
2.81-2.966.50.14610830.9840.0610.1590.98899.7
2.96-3.146.20.11510740.9880.050.1251.00199.3
3.14-3.395.80.08810880.9930.0390.0970.96199
3.39-3.737.10.0710950.9960.0280.0750.95499.8
3.73-4.266.90.06111080.9960.0250.0661.08699.9
4.26-5.376.50.05711300.9970.0240.0621.14199.6
5.37-5060.06211920.9960.0260.0671.12198.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18rc3_3805refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YLM

4ylm


Resolution: 1.97→44.85 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 2000 9.27 %
Rwork0.1817 19569 -
obs0.1845 21569 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.91 Å2 / Biso mean: 30.6956 Å2 / Biso min: 14.78 Å2
Refinement stepCycle: final / Resolution: 1.97→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2096 0 30 161 2287
Biso mean--46.52 38.87 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072193
X-RAY DIFFRACTIONf_angle_d0.8152981
X-RAY DIFFRACTIONf_dihedral_angle_d16.411288
X-RAY DIFFRACTIONf_chiral_restr0.057313
X-RAY DIFFRACTIONf_plane_restr0.005387
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.97-2.020.31211300.25091278140893
2.02-2.080.23991430.21861394153799
2.08-2.140.24481410.198913701511100
2.14-2.210.22621390.19671373151299
2.21-2.280.25871410.19451383152499
2.28-2.380.22731430.188613951538100
2.38-2.480.21991420.185313911533100
2.48-2.610.22051430.194313881531100
2.61-2.780.22591430.19091405154899
2.78-2.990.1991420.187813941536100
2.99-3.290.22031440.18071410155499
3.29-3.770.18321470.162914281575100
3.77-4.750.18171480.150414481596100
4.75-44.850.21931540.19241512166699

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