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- PDB-7u07: Crystal structure of queuine salvage enzyme DUF2419, apo form -

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Basic information

Entry
Database: PDB / ID: 7u07
TitleCrystal structure of queuine salvage enzyme DUF2419, apo form
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 / Queuosine 5'-phosphate N-glycosylase/hydrolase
Function and homology information
Biological speciesSphaerobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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 17, 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)74,3772
Polymers74,3772
Non-polymers00
Water5,188288
1
A: Queuine salvage enzyme DUF2419


Theoretical massNumber of molelcules
Total (without water)37,1891
Polymers37,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Queuine salvage enzyme DUF2419


Theoretical massNumber of molelcules
Total (without water)37,1891
Polymers37,1891
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.752, 105.752, 159.181
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 (strain DSM 20745 / S 6022) (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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.09 Å3/Da / Density % sol: 60.14 % / 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

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21001N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.9795
SYNCHROTRONSSRL BL12-220.97923, 0.95369, 0.97965
Detector
TypeIDDetectorDate
DECTRIS PILATUS 6M1PIXELOct 2, 2020
DECTRIS PILATUS 6M2PIXELFeb 3, 2021
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.979231
30.953691
40.979651
ReflectionResolution: 2.1→40 Å / Num. obs: 52930 / % possible obs: 99.7 % / Redundancy: 115.7 % / Rmerge(I) obs: 0.453 / Rpim(I) all: 0.042 / Rrim(I) all: 0.455 / Χ2: 0.916 / Net I/σ(I): 2.3 / Num. measured all: 6123676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.1470.16.21626010.6370.7366.2610.8599.8
2.14-2.1873.64.625540.7440.5234.6310.84998.6
2.18-2.2291.64.37925990.8060.4524.4030.85799.7
2.22-2.26105.42.72426070.8960.2642.7370.90199.9
2.26-2.31111.12.72726170.9330.2572.7390.86599.8
2.31-2.37116.62.60526030.9340.2392.6160.86399.9
2.37-2.42121.72.27326250.9480.2042.2820.86999.8
2.42-2.49126.72.04726180.9640.1812.0550.86999.7
2.49-2.56127.91.8326210.970.1611.8380.87199.9
2.56-2.65126.41.50826170.9790.1331.5140.87699.9
2.65-2.74121.41.20326230.9860.1091.2080.89599.9
2.74-2.85111.60.92326280.9880.0860.9270.90198.8
2.85-2.98133.30.70426360.9950.0610.7070.902100
2.98-3.141320.52526430.9960.0450.5270.922100
3.14-3.33130.10.36226560.9980.0320.3640.935100
3.33-3.591280.23826830.9990.0210.2390.965100
3.59-3.95120.50.165268710.0150.1660.993100
3.95-4.52119.20.114267310.010.1151.02298.6
4.52-5.7127.90.107274110.0090.1071.009100
5.7-40115.70.073289810.0070.0731.01898.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSvJan31, 2020data scaling
PDB_EXTRACT3.27data extraction
XDSvJan31, 2020data reduction
PHENIXv1.19.2phasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→37.48 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1318 / WRfactor Rwork: 0.11 / FOM work R set: 0.8782 / SU B: 7.823 / SU ML: 0.088 / SU Rfree: 0.1206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1659 2521 4.9 %RANDOM
Rwork0.1343 ---
obs0.1359 48749 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.52 Å2 / Biso mean: 35.095 Å2 / Biso min: 15.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å20 Å20 Å2
2---0.66 Å20 Å2
3---1.32 Å2
Refinement stepCycle: final / Resolution: 2.1→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 0 290 5388
Biso mean---40.96 -
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135350
X-RAY DIFFRACTIONr_bond_other_d0.0030.0144967
X-RAY DIFFRACTIONr_angle_refined_deg1.3031.6387309
X-RAY DIFFRACTIONr_angle_other_deg1.2981.57611320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84419.942345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2451565
X-RAY DIFFRACTIONr_chiral_restr0.060.2673
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026232
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021410
X-RAY DIFFRACTIONr_rigid_bond_restr1.948310317
LS refinement shellResolution: 2.101→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 172 -
Rwork0.26 3433 -
all-3605 -
obs--93.25 %

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