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- PDB-5t8y: Structure of epoxyqueuosine reductase from Bacillus subtilis with... -

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Basic information

Entry
Database: PDB / ID: 5t8y
TitleStructure of epoxyqueuosine reductase from Bacillus subtilis with the Asp134 catalytic loop swung out of the active site.
Components
  • Epoxyqueuosine reductase
  • RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
KeywordsOXIDOREDUCTASE/RNA / B12 / cobalamin / iron sulfur cluster / tRNA modifying enzyme / OXIDOREDUCTASE-RNA complex
Function / homology
Function and homology information


epoxyqueuosine reductase / epoxyqueuosine reductase activity / tRNA modification / tRNA queuosine(34) biosynthetic process / 4 iron, 4 sulfur cluster binding / metal ion binding / cytoplasm
Similarity search - Function
Epoxyqueuosine reductase QueG / Epoxyqueuosine reductase QueG, DUF1730 / PBS lyase HEAT-like repeat / Epoxyqueuosine reductase QueG, DUF1730 / 4Fe-4S double cluster binding domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / HEAT repeats / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. ...Epoxyqueuosine reductase QueG / Epoxyqueuosine reductase QueG, DUF1730 / PBS lyase HEAT-like repeat / Epoxyqueuosine reductase QueG, DUF1730 / 4Fe-4S double cluster binding domain / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / HEAT repeats / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
COBALAMIN / PHOSPHATE ION / IRON/SULFUR CLUSTER / RNA / RNA (> 10) / Epoxyqueuosine reductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.653 Å
AuthorsDowling, D.P. / Miles, Z.D. / Kohrer, C. / Maiocco, S.J. / Elliott, S.J. / Bandarian, V. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM72623 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Molecular basis of cobalamin-dependent RNA modification.
Authors: Dowling, D.P. / Miles, Z.D. / Kohrer, C. / Maiocco, S.J. / Elliott, S.J. / Bandarian, V. / Drennan, C.L.
History
DepositionSep 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epoxyqueuosine reductase
B: Epoxyqueuosine reductase
X: RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,63316
Polymers102,9013
Non-polymers4,73213
Water25214
1
A: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9606
Polymers48,7371
Non-polymers2,2245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17410 Å2
MethodPISA
2
B: Epoxyqueuosine reductase
X: RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,67210
Polymers54,1642
Non-polymers2,5088
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.763, 111.030, 95.971
Angle α, β, γ (deg.)90.000, 99.130, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 3 molecules ABX

#1: Protein Epoxyqueuosine reductase / Queuosine biosynthesis protein QueG


Mass: 48736.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: queG, ygaP, yhbA, BSU08910 / Production host: Escherichia coli (E. coli) / References: UniProt: P97030, epoxyqueuosine reductase
#2: RNA chain RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')


Mass: 5427.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: anticodon stem loop of Tyr-tRNA from E. coli / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 27 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M acetate (pH 4.5), 0.4 M (NH4)H2PO4, 12% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 25487 / % possible obs: 95.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 12
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 1.95 / % possible all: 79

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D08

5d08


Resolution: 2.653→47.9 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.25 / Phase error: 37.27
RfactorNum. reflection% reflection
Rfree0.2665 1252 4.93 %
Rwork0.2376 --
obs0.2391 25389 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.46 Å2 / Biso mean: 71.4087 Å2 / Biso min: 58.02 Å2
Refinement stepCycle: final / Resolution: 2.653→47.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5871 107 249 14 6241
Biso mean--69.4 66.93 -
Num. residues----751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036401
X-RAY DIFFRACTIONf_angle_d0.7078772
X-RAY DIFFRACTIONf_chiral_restr0.027947
X-RAY DIFFRACTIONf_plane_restr0.0031127
X-RAY DIFFRACTIONf_dihedral_angle_d10.4842548
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6533-2.75950.40711010.36012193229477
2.7595-2.88510.40411240.34482403252786
2.8851-3.03720.39311390.35162669280894
3.0372-3.22750.35461460.31662757290397
3.2275-3.47660.33241420.292728192961100
3.4766-3.82630.27491540.2432790294499
3.8263-4.37970.25031580.21942799295799
4.3797-5.51660.23621480.198328472995100
5.5166-47.90730.19981400.18892860300099

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