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- PDB-5d0b: Crystal structure of epoxyqueuosine reductase with a tRNA-TYR epo... -

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Basic information

Entry
Database: PDB / ID: 5d0b
TitleCrystal structure of epoxyqueuosine reductase with a tRNA-TYR epoxyqueuosine-modified tRNA stem loop
Components
  • Epoxyqueuosine reductase
  • RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
Keywordsoxidoreductase/RNA / B12 / tRNA modification / HEAT-domain / queuosine / 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 / 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. ...Epoxyqueuosine reductase QueG / Epoxyqueuosine reductase QueG, DUF1730 / 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: 2.645 Å
AuthorsDowling, D.P. / Miles, Z.D. / Kohrer, C. / Bandarian, V. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM72623 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
DepositionAug 3, 2015Deposition 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 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

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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
F: RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,37612
Polymers103,0273
Non-polymers4,3499
Water1,26170
1
A: Epoxyqueuosine reductase
F: RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5117
Polymers54,2902
Non-polymers2,2215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-69 kcal/mol
Surface area18310 Å2
MethodPISA
2
B: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8655
Polymers48,7371
Non-polymers2,1294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-55 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.644, 110.754, 99.223
Angle α, β, γ (deg.)90.000, 95.160, 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 ABF

#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 / Plasmid: pASK-IBA43plus / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P97030, epoxyqueuosine reductase
#2: RNA chain RNA (5'-D(*GP*CP*AP*GP*AP*CP*UP*(56B)P*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')


Mass: 5553.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized by IDT and enzymatically modified / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 5 types, 79 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.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (0.1 M acetate (pH 4.5), 0.4 M (NH4)H2PO4, 12% (w/v) PEG 3350
Temp details: anaerobic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.645→100 Å / Num. obs: 26382 / % possible obs: 92.8 % / Redundancy: 5.3 % / Biso Wilson estimate: 37.76 Å2 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.067 / Rrim(I) all: 0.169 / Χ2: 1.108 / Net I/av σ(I): 10 / Net I/σ(I): 5.3 / Num. measured all: 138854
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.65-2.743.30.33719220.8730.1940.3920.89768.3
2.74-2.8550.34722860.9240.1520.3810.90280.4
2.85-2.985.20.3325100.930.1430.3610.9288.7
2.98-3.145.10.26627340.9620.1170.2921.10297.2
3.14-3.345.40.22328030.9690.0960.2441.15598.7
3.34-3.65.60.18728070.9790.0790.2041.16299.3
3.6-3.965.40.15428010.9820.0670.1691.26298.4
3.96-4.535.80.13528270.9850.0570.1471.21398.8
4.53-5.715.60.12228310.9840.0530.1341.13798.7
5.71-1005.60.10228610.9890.0450.1121.10298.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D08

5d08


Resolution: 2.645→32.049 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2214 1316 5 %Random selection
Rwork0.1917 25013 --
obs0.1932 26329 91.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.55 Å2 / Biso mean: 31.4805 Å2 / Biso min: 16.2 Å2
Refinement stepCycle: final / Resolution: 2.645→32.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5903 368 230 70 6571
Biso mean--25.01 27.25 -
Num. residues----768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046712
X-RAY DIFFRACTIONf_angle_d0.7289211
X-RAY DIFFRACTIONf_chiral_restr0.0341018
X-RAY DIFFRACTIONf_plane_restr0.0041165
X-RAY DIFFRACTIONf_dihedral_angle_d10.9532734
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 (%)
2.6454-2.75120.307980.24411866196462
2.7512-2.87640.2911280.24932427255580
2.8764-3.02790.29311440.25652729287390
3.0279-3.21740.26231540.24272955310998
3.2174-3.46560.27341570.22342991314899
3.4656-3.81380.19771590.17763019317899
3.8138-4.36450.22311580.16752979313799
4.3645-5.49440.18821580.16223000315899
5.4944-32.05150.16841600.16213047320799

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