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- PDB-7u91: Crystal structure of queuine salvage enzyme DUF2419, in complex w... -

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Basic information

Entry
Database: PDB / ID: 7u91
TitleCrystal structure of queuine salvage enzyme DUF2419, in complex with queuosine-5'-monophosphate
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 / Chem-56B / AMMONIUM ION / DI(HYDROXYETHYL)ETHER / Queuosine 5'-phosphate N-glycosylase/hydrolase
Function and homology information
Biological speciesSphaerobacter thermophilus DSM 20745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 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
DepositionMar 9, 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)75,4987
Polymers74,3772
Non-polymers1,1215
Water3,369187
1
A: Queuine salvage enzyme DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6963
Polymers37,1891
Non-polymers5072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Queuine salvage enzyme DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8024
Polymers37,1891
Non-polymers6143
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.628, 105.628, 159.585
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-56B / 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-7-(5-O-phosphono-beta-D-ribofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one


Type: RNA linking / Mass: 489.374 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N5O10P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H4N
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.99 Å3/Da / Density % sol: 58.9 % / 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: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35946 / % possible obs: 99.7 % / Redundancy: 23 % / Rmerge(I) obs: 0.308 / Rpim(I) all: 0.064 / Rrim(I) all: 0.315 / Χ2: 0.9 / Net I/σ(I): 3 / Num. measured all: 827080
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4411.32.68817330.3380.8262.8180.88899.5
2.44-2.4913.72.62217680.3320.7272.7240.91199.4
2.49-2.5316.32.71417500.4510.6872.8010.90599.7
2.53-2.5919.12.47817710.5310.5772.5450.90199.9
2.59-2.6421.12.26317720.6140.52.3180.91199.9
2.64-2.722.52.0417680.7010.4362.0870.91499.9
2.7-2.7722.71.86817750.7520.3971.910.92499.9
2.77-2.8522.51.75117660.7220.3721.7920.93899.5
2.85-2.9326.81.33917800.8850.2591.3640.92499.9
2.93-3.0226.71.07417830.9230.2081.0940.93799.9
3.02-3.1326.60.88817800.9340.1720.9050.95399.8
3.13-3.2626.40.67117880.9530.1310.6840.95799.9
3.26-3.4126.20.49117990.9750.0970.50.953100
3.41-3.5825.10.35517870.9810.0720.3620.983100
3.58-3.8124.50.25617860.9870.0520.2620.97498.7
3.81-4.127.10.20918130.9930.040.2130.942100
4.1-4.5226.60.15818300.9960.0310.1610.911100
4.52-5.1725.30.13318460.9970.0260.1360.836100
5.17-6.5124.80.12918570.9970.0260.1320.75999
6.51-50240.07419940.9950.0150.0760.59799

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Processing

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

7u07


Resolution: 2.4→47.56 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.1673 / WRfactor Rwork: 0.1247 / FOM work R set: 0.9173 / SU B: 12.584 / SU ML: 0.118 / SU Rfree: 0.1801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1673 1580 5 %RANDOM
Rwork0.1247 ---
obs0.1268 30242 88.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.1 Å2 / Biso mean: 41.594 Å2 / Biso min: 19.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å2-0 Å20 Å2
2---1.08 Å20 Å2
3---2.16 Å2
Refinement stepCycle: final / Resolution: 2.4→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 75 187 5360
Biso mean--47.13 46.6 -
Num. residues----642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135365
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154952
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.657332
X-RAY DIFFRACTIONr_angle_other_deg1.2751.58311290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3455652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.19920.03336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.14315795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9011562
X-RAY DIFFRACTIONr_chiral_restr0.0610.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026150
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021388
X-RAY DIFFRACTIONr_rigid_bond_restr1.647310316
LS refinement shellResolution: 2.401→2.463 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 23 -
Rwork0.225 455 -
all-478 -
obs--18.46 %

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