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- PDB-6pup: 1.9 A crystal structure of flavodoxin-like domain of Schizosaccha... -

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Basic information

Entry
Database: PDB / ID: 6pup
Title1.9 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 / metal binding
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
FLAVIN MONONUCLEOTIDE / : / tRNA 4-demethylwyosine synthase (AdoMet-dependent)
Similarity search - Component
Biological speciesSchizosaccharomyces japonicus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.89 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 29, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / struct
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _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

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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)20,3174
Polymers19,7501
Non-polymers5663
Water82946
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)62.268, 58.632, 62.520
Angle α, β, γ (deg.)90.000, 118.710, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

#1: Protein Wybutosine biosynthesis protein Tyw1


Mass: 19750.379 Da / Num. of mol.: 1 / Fragment: Flavodoxin-like domain, residues 76-251
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
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.53 Å3/Da / Density % sol: 51.46 % / Description: yellow tetragonal crystals, 150 x 50 x 50 um3
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM Hepes-NaOH pH 7.5, 100 mM MOPS pH 7.5, 9.37% v/v MPD, 9.37% PEG1000, 9.37% w/v PEG 3350, 300 mM MgCl2 x 6 H20; 300 mM CaCl2 x 2 H20

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→54.83 Å / Num. obs: 10359 / % possible obs: 77.4 % / Redundancy: 6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.051 / Rrim(I) all: 0.126 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.053.60.9782740.4760.5711.1428.5
1.89-8.9860.0491620.9990.0220.05499.3

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.89→54.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.146 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.188
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1081 10.1 %RANDOM
Rwork0.1704 ---
obs0.1754 9600 67.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.18 Å2 / Biso mean: 27.357 Å2 / Biso min: 4.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å20 Å2-0.41 Å2
2---0.72 Å20 Å2
3---1.98 Å2
Refinement stepCycle: final / Resolution: 1.89→54.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1339 0 33 46 1418
Biso mean--17.44 33.22 -
Num. residues----169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131404
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171282
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.6671910
X-RAY DIFFRACTIONr_angle_other_deg1.3581.5892964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4285170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88523.15173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.85815230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.022157
X-RAY DIFFRACTIONr_chiral_restr0.0740.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
LS refinement shellResolution: 1.891→1.94 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 12 -
Rwork0.325 99 -
all-111 -
obs--9.49 %

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