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- PDB-5d0a: Crystal structure of epoxyqueuosine reductase with cleaved RNA st... -

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Basic information

Entry
Database: PDB / ID: 5d0a
TitleCrystal structure of epoxyqueuosine reductase with cleaved RNA stem loop
Components
  • Epoxyqueuosine reductase
  • RNA (5'-R(*G*CP*AP*GP*AP*CP*UP*GP*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 / 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: 2.1 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, GM17151 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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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
C: Epoxyqueuosine reductase
D: Epoxyqueuosine reductase
E: RNA (5'-R(*G*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
F: RNA (5'-R(*G*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)214,68426
Polymers205,8016
Non-polymers8,88320
Water14,304794
1
A: Epoxyqueuosine reductase
F: RNA (5'-R(*G*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)56,3857
Polymers54,1642
Non-polymers2,2215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-65 kcal/mol
Surface area18370 Å2
MethodPISA
2
B: Epoxyqueuosine reductase
E: RNA (5'-R(*G*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)56,3857
Polymers54,1642
Non-polymers2,2215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-65 kcal/mol
Surface area18220 Å2
MethodPISA
3
C: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9576
Polymers48,7371
Non-polymers2,2215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-57 kcal/mol
Surface area16300 Å2
MethodPISA
4
D: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9576
Polymers48,7371
Non-polymers2,2215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-56 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.587, 111.118, 96.008
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / RNA chain , 2 types, 6 molecules ABCDEF

#1: Protein
Epoxyqueuosine reductase / Queuosine biosynthesis protein QueG


Mass: 48736.641 Da / Num. of mol.: 4
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'-R(*G*CP*AP*GP*AP*CP*UP*GP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')


Mass: 5427.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthesized by IDT / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 5 types, 814 molecules

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


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / 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: 2.27 Å3/Da / Density % sol: 45.79 % / Description: square pyramidal
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: (0.1 M acetate, 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: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 104237 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.15 Å2 / Rsym value: 0.081 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.394 / % possible all: 89.3

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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: 2.1→46.39 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 5106 4.91 %Random selection
Rwork0.184 ---
obs0.186 103951 97.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11832 507 472 794 13605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913259
X-RAY DIFFRACTIONf_angle_d1.08818146
X-RAY DIFFRACTIONf_dihedral_angle_d13.4725355
X-RAY DIFFRACTIONf_chiral_restr0.0442001
X-RAY DIFFRACTIONf_plane_restr0.0062300
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.34441370.27272798X-RAY DIFFRACTION84
2.1239-2.14890.31281390.27163099X-RAY DIFFRACTION90
2.1489-2.17510.30451290.25643108X-RAY DIFFRACTION91
2.1751-2.20260.28961630.24653138X-RAY DIFFRACTION94
2.2026-2.23160.28621520.23613302X-RAY DIFFRACTION97
2.2316-2.26210.31281610.22923348X-RAY DIFFRACTION98
2.2621-2.29450.25431620.22183306X-RAY DIFFRACTION99
2.2945-2.32870.24741970.2063337X-RAY DIFFRACTION99
2.3287-2.36510.24611710.20363317X-RAY DIFFRACTION99
2.3651-2.40390.26491920.20963324X-RAY DIFFRACTION99
2.4039-2.44530.28881920.20143351X-RAY DIFFRACTION99
2.4453-2.48980.27022080.20613245X-RAY DIFFRACTION99
2.4898-2.53770.25821800.19383322X-RAY DIFFRACTION98
2.5377-2.58950.27351680.19233338X-RAY DIFFRACTION98
2.5895-2.64580.23061610.18653252X-RAY DIFFRACTION96
2.6458-2.70730.23341740.18163337X-RAY DIFFRACTION98
2.7073-2.7750.25581650.18473367X-RAY DIFFRACTION99
2.775-2.850.21141950.18783351X-RAY DIFFRACTION99
2.85-2.93390.24231840.19733356X-RAY DIFFRACTION99
2.9339-3.02850.2561490.19623362X-RAY DIFFRACTION99
3.0285-3.13680.23781960.20853340X-RAY DIFFRACTION99
3.1368-3.26230.25191700.2013357X-RAY DIFFRACTION99
3.2623-3.41080.24481770.20153266X-RAY DIFFRACTION97
3.4108-3.59050.24271540.17763344X-RAY DIFFRACTION98
3.5905-3.81540.20691830.16063370X-RAY DIFFRACTION100
3.8154-4.10980.16721800.15643394X-RAY DIFFRACTION99
4.1098-4.52310.161370.14063417X-RAY DIFFRACTION99
4.5231-5.17680.19061620.14043299X-RAY DIFFRACTION97
5.1768-6.51940.19671940.16383396X-RAY DIFFRACTION99
6.5194-46.40210.18051740.1723304X-RAY DIFFRACTION95

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