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- PDB-6puq: 1.56 A crystal structure of flavodoxin-like domain of Schizosacch... -

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Basic information

Entry
Database: PDB / ID: 6puq
Title1.56 A crystal structure of flavodoxin-like domain of Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN
ComponentsWybutosine biosynthesis protein Tyw1
KeywordsFLAVOPROTEIN / tRNA / hypermodification / wyosine
Function / homology
Function and homology information


tRNA 4-demethylwyosine synthase (AdoMet-dependent) / tRNA-4-demethylwyosine synthase activity / wybutosine biosynthetic process / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding
Similarity search - Function
tRNA wybutosine-synthesis / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / Wyosine base formation / Flavodoxin, conserved site / Flavodoxin signature. / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Flavodoxin / Flavodoxin-like domain profile. ...tRNA wybutosine-synthesis / S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase / Wyosine base formation / Flavodoxin, conserved site / Flavodoxin signature. / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Flavodoxin / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Aldolase-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / DI(HYDROXYETHYL)ETHER / tRNA 4-demethylwyosine synthase (AdoMet-dependent)
Similarity search - Component
Biological speciesSchizosaccharomyces japonicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsSjekloca, L. / Ferre-D'Amare, A.R.
CitationJournal: MicroPubl Biol / Year: 2022
Title: Biochemical and structural characterization of the flavodoxin-like domain of the Schizosaccharomyces japonicus putative tRNAPhe 4-demethylwyosine synthase Tyw1 in complex with FMN.
Authors: Sjekloca, L. / Ferre-D'Amare, A.R.
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Advisory / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / struct
Item: _audit_author.name / _citation.journal_abbrev ..._audit_author.name / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Wybutosine biosynthesis protein Tyw1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5159
Polymers24,7721
Non-polymers7438
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.298, 73.087, 42.518
Angle α, β, γ (deg.)90.000, 91.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Wybutosine biosynthesis protein Tyw1


Mass: 24772.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces japonicus (strain yFS275 / FY16936) (yeast)
Strain: yFS275 / FY16936 / Gene: SJAG_04265 / Production host: Escherichia coli (E. coli) / References: UniProt: B6K6D6

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Non-polymers , 5 types, 72 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.77 Å3/Da / Density % sol: 30.66 %
Description: yellow pyramidal or tetragonal crystals 300 x 300 x 300 um3
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200 mM sodium acetate trihydrate, 30% PEG 4000, 100 mM Tris- HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→73.09 Å / Num. obs: 41931 / % possible obs: 87.9 % / Redundancy: 5.7 % / Biso Wilson estimate: 21.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.033 / Rrim(I) all: 0.082 / Net I/σ(I): 11.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.56-1.63.40.9787430.6120.6121.16241.5
1.56-6.986.20.0582910.9930.0260.06499.8

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→42.496 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.94
RfactorNum. reflection% reflection
Rfree0.2271 3866 9.22 %
Rwork0.1963 --
obs0.1992 41931 86.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.25 Å2 / Biso mean: 29.2538 Å2 / Biso min: 11.57 Å2
Refinement stepCycle: final / Resolution: 1.56→42.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 47 64 1469
Biso mean--31.84 36.99 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061545
X-RAY DIFFRACTIONf_angle_d0.8592111
X-RAY DIFFRACTIONf_chiral_restr0.049236
X-RAY DIFFRACTIONf_plane_restr0.004267
X-RAY DIFFRACTIONf_dihedral_angle_d16.856936
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.56-1.61580.53541760.4552177540
1.6158-1.68050.42692480.3843246856
1.6805-1.75690.37183600.356334377
1.7569-1.84960.29884200.2866415794
1.8496-1.96550.29564400.2402435099
1.9655-2.11720.24124500.2032440799
2.1172-2.33030.22764430.18744364100
2.3303-2.66740.1994370.18814409100
2.6674-3.36040.21384540.18424380100
3.3604-42.4960.19074380.15964412100

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