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- PDB-7u1o: Crystal structure of queuine salvage enzyme DUF2419 complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7u1o
TitleCrystal structure of queuine salvage enzyme DUF2419 complexed with queuosine
ComponentsQueuine salvage enzyme DUF2419
KeywordsHYDROLASE / 7-deazaguanine salvage / queuosine / tRNA modification
Function / homologyQueuosine salvage protein family / Queuosine salvage protein / : / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / MALONATE ION / DI(HYDROXYETHYL)ETHER / Chem-QEO / Queuosine 5'-phosphate N-glycosylase/hydrolase
Function and homology information
Biological speciesSphaerobacter thermophilus DSM 20745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å
AuthorsHung, S.-H. / Swairjo, M.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM70641 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM110588-06A1 United States
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate.
Authors: Hung, S.H. / Elliott, G.I. / Ramkumar, T.R. / Burtnyak, L. / McGrenaghan, C.J. / Alkuzweny, S. / Quaiyum, S. / Iwata-Reuyl, D. / Pan, X. / Green, B.D. / Kelly, V.P. / de Crecy-Lagard, V. / Swairjo, M.A.
History
DepositionFeb 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Queuine salvage enzyme DUF2419
B: Queuine salvage enzyme DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5067
Polymers74,3772
Non-polymers1,1295
Water4,810267
1
A: Queuine salvage enzyme DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7003
Polymers37,1891
Non-polymers5112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Queuine salvage enzyme DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8064
Polymers37,1891
Non-polymers6183
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.663, 105.663, 157.742
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Queuine salvage enzyme DUF2419


Mass: 37188.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria)
Strain: DSM 20745 / S 6022 / Gene: Sthe_2331 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: D1C7A6
#2: Chemical ChemComp-QEO / 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-beta-D-ribofuranosyl-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one


Mass: 409.394 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H23N5O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.96 Å3/Da / Density % sol: 58.4 % / Description: Long, thin clustered crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1 M Sodium malonate, 0.1 M HEPES, 0.5% (v/v) Jaffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.03317 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 2.35→23 Å / Num. obs: 38007 / % possible obs: 100 % / Redundancy: 32.2 % / Rmerge(I) obs: 0.389 / Rpim(I) all: 0.069 / Rrim(I) all: 0.395 / Χ2: 1.059 / Net I/σ(I): 2.7 / Num. measured all: 1222832
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.35-2.3916.84.26818640.2561.0554.4011.061100
2.39-2.4319.83.83818510.4040.8693.9371.051100
2.43-2.4824.13.29318470.5070.6733.3631.062100
2.48-2.5327.62.77518850.6270.5312.8261.064100
2.53-2.5929.12.61418760.6550.4882.661.069100
2.59-2.6530.32.26718660.7530.4172.3061.064100
2.65-2.7134.71.95818680.8460.3321.9861.081100
2.71-2.7936.81.57618830.8780.2581.5981.074100
2.79-2.8736.71.28118780.920.211.2981.081100
2.87-2.9636.41.05318630.9470.1741.0671.07799.9
2.96-3.0736.40.82318840.9620.1360.8341.066100
3.07-3.1935.80.69418850.9740.1160.7041.062100
3.19-3.3334.10.4819020.9870.0830.4871.074100
3.33-3.5132.60.34918880.9910.0620.3551.094100
3.51-3.7337.50.25119080.9960.0410.2551.073100
3.73-4.01370.19919080.9980.0330.2021.067100
4.01-4.4136.10.13919420.9990.0230.1411.032100
4.41-5.0532.40.11419410.9990.020.1161.012100
5.05-6.3435.70.12819740.9990.0220.130.995100
6.34-2332.70.07820940.9990.0140.081.025100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000v721.3data reduction
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7U07

7u07


Resolution: 2.35→22.98 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1461 / WRfactor Rwork: 0.1093 / FOM work R set: 0.8419 / SU B: 14.108 / SU ML: 0.134 / SU Rfree: 0.1745 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1793 1790 5 %RANDOM
Rwork0.1352 ---
obs0.1373 34207 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.83 Å2 / Biso mean: 39.108 Å2 / Biso min: 20.19 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å20 Å2
2---2.65 Å20 Å2
3---5.3 Å2
Refinement stepCycle: final / Resolution: 2.35→22.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 79 267 5440
Biso mean--46.78 43.6 -
Num. residues----641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135343
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154950
X-RAY DIFFRACTIONr_angle_refined_deg1.41.6577290
X-RAY DIFFRACTIONr_angle_other_deg1.271.58611280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.98119.851336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48715796
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8811564
X-RAY DIFFRACTIONr_chiral_restr0.0560.2680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026135
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021383
X-RAY DIFFRACTIONr_rigid_bond_restr3.227310292
LS refinement shellResolution: 2.35→2.409 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.368 60 -
Rwork0.324 1236 -
obs--46.94 %

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