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- PDB-5d6s: Structure of epoxyqueuosine reductase from Streptococcus thermophilus. -

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Basic information

Entry
Database: PDB / ID: 5d6s
TitleStructure of epoxyqueuosine reductase from Streptococcus thermophilus.
ComponentsEpoxyqueuosine reductase
KeywordsOXIDOREDUCTASE / cobalamin dependent oxidoreductase / iron-sulfur protein / tRNA-binding
Function / homology
Function and homology information


queuosine biosynthetic process / tRNA processing / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / metal ion binding / cytoplasm
Similarity search - Function
Epoxyqueuosine reductase QueG / Epoxyqueuosine reductase QueG, DUF1730 / Epoxyqueuosine reductase QueG, DUF1730 / 4Fe-4S double cluster binding domain / Alpha-helical ferredoxin / 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-type fold
Similarity search - Domain/homology
COBALAMIN / IRON/SULFUR CLUSTER / : / Epoxyqueuosine reductase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsPayne, K.A.P. / Fisher, K. / Dunstan, M.S. / Sjuts, H. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research CouncilDEHALORES206080 United Kingdom
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Epoxyqueuosine Reductase Structure Suggests a Mechanism for Cobalamin-dependent tRNA Modification.
Authors: Payne, K.A. / Fisher, K. / Sjuts, H. / Dunstan, M.S. / Bellina, B. / Johannissen, L. / Barran, P. / Hay, S. / Rigby, S.E. / Leys, D.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3May 8, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _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: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,84220
Polymers225,6745
Non-polymers10,16815
Water1,33374
1
A: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1684
Polymers45,1351
Non-polymers2,0343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1684
Polymers45,1351
Non-polymers2,0343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1684
Polymers45,1351
Non-polymers2,0343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1684
Polymers45,1351
Non-polymers2,0343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1684
Polymers45,1351
Non-polymers2,0343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.120, 106.120, 332.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15B
25C
16B
26D
17B
27E
18C
28D
19C
29E
110D
210E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A29 - 400
2010B29 - 400
1020A32 - 399
2020C32 - 399
1030A29 - 400
2030D29 - 400
1040A29 - 400
2040E29 - 400
1050B32 - 399
2050C32 - 399
1060B29 - 400
2060D29 - 400
1070B29 - 400
2070E29 - 400
1080C32 - 399
2080D32 - 399
1090C32 - 399
2090E32 - 399
10100D29 - 400
20100E29 - 400

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

#1: Protein
Epoxyqueuosine reductase


Mass: 45134.793 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: MNA02_1104 / Production host: Bacillus megaterium (bacteria) / References: UniProt: A0A0F7K4Z9, UniProt: A0A0R4I997*PLUS
#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: Anaerobic crystals were obtained by mixing 2 microL protein with 2 microL 0.3 M sodium acetate, 0.1 M Tris/Cl pH7.5, 15% w/v PEG4000 and incubated at room temperature in a 100% N2-atmosphere glove box

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.65→88.58 Å / Num. obs: 60261 / % possible obs: 98.8 % / Redundancy: 14 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 17.6
Reflection shellResolution: 2.65→2.72 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 2 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
xia2data reduction
xia2data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→88.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.827 / SU ML: 0.277 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25301 3165 5 %RANDOM
Rwork0.21407 ---
obs0.21601 60261 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.351 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å21.9 Å20 Å2
2--1.9 Å20 Å2
3----6.17 Å2
Refinement stepCycle: 1 / Resolution: 2.65→88.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14536 0 535 74 15145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01915476
X-RAY DIFFRACTIONr_bond_other_d0.0050.0214909
X-RAY DIFFRACTIONr_angle_refined_deg1.9762.02521413
X-RAY DIFFRACTIONr_angle_other_deg1.785334421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61151837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59524.798644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.524152799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6581580
X-RAY DIFFRACTIONr_chiral_restr0.0820.22311
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117383
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A236020.03
12B236020.03
21A232630.02
22C232630.02
31A236040.02
32D236040.02
41A235930.03
42E235930.03
51B232750.01
52C232750.01
61B236260.01
62D236260.01
71B236000.02
72E236000.02
81C232900.01
82D232900.01
91C232780.02
92E232780.02
101D236250.01
102E236250.01
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 242 -
Rwork0.325 4332 -
obs--98.22 %

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