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- PDB-5d08: Crystal structure of selenomethionine-labeled epoxyqueuosine reductase -

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Basic information

Entry
Database: PDB / ID: 5d08
TitleCrystal structure of selenomethionine-labeled epoxyqueuosine reductase
ComponentsEpoxyqueuosine reductase
KeywordsOXIDOREDUCTASE / B12 / tRNA modification / HEAT-domain / queuosine
Function / homology
Function and homology information


epoxyqueuosine reductase / epoxyqueuosine reductase activity / queuosine biosynthetic process / tRNA processing / 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 / Epoxyqueuosine reductase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.747 Å
AuthorsDowling, D.P. / Miles, Z.D. / Kohrer, C. / 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
DepositionAug 2, 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
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,92314
Polymers98,4112
Non-polymers4,51212
Water11,494638
1
A: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5578
Polymers49,2061
Non-polymers2,3517
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Epoxyqueuosine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3676
Polymers49,2061
Non-polymers2,1615
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.301, 95.780, 111.175
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Epoxyqueuosine reductase / Queuosine biosynthesis protein QueG


Mass: 49205.586 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

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Non-polymers , 6 types, 650 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.28 Å3/Da / Density % sol: 46.06 % / Description: square pyramidal
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: APS / Beamline: 24-ID-C / Wavelength: 0.9795, 0.9793, 0.9421
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.94211
ReflectionResolution: 1.747→50 Å / Num. obs: 86822 / % possible obs: 94.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 18.35 Å2 / Rmerge(I) obs: 0.084 / Χ2: 1.018 / Net I/av σ(I): 14.032 / Net I/σ(I): 6.3 / Num. measured all: 404248
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.814.30.57884020.97493
1.81-1.894.60.44685400.98894.3
1.89-1.974.70.33787251.01696.3
1.97-2.074.60.24386771.03295.9
2.07-2.24.50.17384401.0392.8
2.2-2.384.80.13388701.03297.2
2.38-2.614.80.10587961.01796.5
2.61-2.994.70.08185471.06793
2.99-3.774.80.05789611.0396.9
3.77-504.70.04788640.98492.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.747→46.407 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 4338 5.01 %Random selection
Rwork0.1673 82241 --
obs0.1688 86579 94.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.13 Å2 / Biso mean: 28.0559 Å2 / Biso min: 9.62 Å2
Refinement stepCycle: final / Resolution: 1.747→46.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5962 0 238 638 6838
Biso mean--18.79 36.33 -
Num. residues----759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056443
X-RAY DIFFRACTIONf_angle_d0.9548779
X-RAY DIFFRACTIONf_chiral_restr0.039955
X-RAY DIFFRACTIONf_plane_restr0.0051161
X-RAY DIFFRACTIONf_dihedral_angle_d13.0032593
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7474-1.76730.32591450.27522549269490
1.7673-1.78810.27961180.26942700281893
1.7881-1.80990.30481140.25832603271790
1.8099-1.83280.25641510.23472571272290
1.8328-1.85690.25341500.2162760291096
1.8569-1.88240.24831320.20752767289995
1.8824-1.90930.23681750.19842711288696
1.9093-1.93780.25861410.1962746288796
1.9378-1.9680.20851490.19462775292496
1.968-2.00030.22831510.18062721287295
2.0003-2.03480.2151330.17482763289696
2.0348-2.07180.21761450.16942747289296
2.0718-2.11170.21251520.16362748290095
2.1117-2.15480.23211480.16392711285994
2.1548-2.20160.21221290.16142551268089
2.2016-2.25280.20061480.15512794294297
2.2528-2.30920.19111600.15772777293797
2.3092-2.37160.20111500.1582823297397
2.3716-2.44140.19841450.16032797294297
2.4414-2.52020.2051370.1592811294896
2.5202-2.61020.20181440.16332777292196
2.6102-2.71470.15831500.16662733288394
2.7147-2.83830.19591290.16212542267187
2.8383-2.98790.18691430.17762852299597
2.9879-3.1750.19181390.17612860299998
3.175-3.42010.17281390.1682842298197
3.4201-3.76420.1661540.14872832298696
3.7642-4.30850.16581530.13792623277689
4.3085-5.42690.17171760.14122907308398
5.4269-46.42310.18221380.16422848298690
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7280.0526-0.2691.2926-0.18932.25980.0826-0.10340.09070.4159-0.05970.0634-0.4383-0.0201-0.03650.312-0.0267-0.01750.173-0.0040.191550.172171.719685.7336
20.45580.8460.49081.8333-0.46742.80050.040.0213-0.03910.2884-0.03880.02390.198-0.07340.1250.22640.0036-0.02060.13180.03310.177547.553352.697679.9042
30.39450.2488-0.14731.4472-0.36851.42050.0458-0.03440.01190.1751-0.0882-0.1301-0.08480.17140.00210.15820.0072-0.03290.16560.01030.152656.498563.04876.9517
40.5250.24580.20120.75590.43954.5591-0.05140.0531-0.0465-0.1461-0.0113-0.00420.2508-0.18850.06370.21270.0078-0.00180.1314-0.01610.164244.941251.214652.0409
55.6281-4.9157-4.96295.13754.73455.46550.2798-0.21650.5431-0.25670.0313-0.1089-0.3808-0.008-0.29050.20260.02010.0360.1097-0.00690.091160.030153.424636.9659
60.62840.0365-0.05611.7784-0.28072.34930.0314-0.07730.06730.3835-0.05390.0673-0.37510.01030.01720.3269-0.0437-0.01260.1844-0.00530.207992.17868.010286.1058
70.94030.1137-0.57272.48470.5223.70980.07120.0227-0.03360.1971-0.05480.05210.1753-0.04720.04850.3027-0.0185-0.02380.14180.02950.19589.036149.990680.6386
80.70620.0505-0.30261.4421-0.01462.126-0.0039-0.0535-0.01030.1117-0.0267-0.129-0.02230.27170.02020.2084-0.0185-0.02380.17340.01660.17998.71259.482776.8701
90.8728-0.09490.23430.90290.69864.1484-0.02390.0824-0.0148-0.1140.0006-0.00680.2405-0.09130.02540.2778-0.0262-0.00030.1406-0.00850.180687.584447.999151.4368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:79)A2 - 79
2X-RAY DIFFRACTION2(chain A and resid 80:125)A80 - 125
3X-RAY DIFFRACTION3(chain A and resid 126:264)A126 - 264
4X-RAY DIFFRACTION4(chain A and resid 265:369)A265 - 369
5X-RAY DIFFRACTION5(chain A and resid 370:385)A370 - 385
6X-RAY DIFFRACTION6(chain B and resid 2:79)B2 - 79
7X-RAY DIFFRACTION7(chain B and resid 80:126)B80 - 126
8X-RAY DIFFRACTION8(chain B and resid 127:264)B127 - 264
9X-RAY DIFFRACTION9(chain B and resid 265:376)B265 - 376

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