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- PDB-8dl3: Crystal structure of the human queuine salvage enzyme DUF2419, co... -

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Basic information

Entry
Database: PDB / ID: 8dl3
TitleCrystal structure of the human queuine salvage enzyme DUF2419, complexed with queuine
ComponentsQueuosine salvage protein
KeywordsHYDROLASE / 7-deazaguanine salvage / queuosine / tRNA modification
Function / homologyQueuosine salvage protein family / Queuosine salvage protein / nucleoside salvage / : / Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds / hydrolase activity / Chem-QEI / Queuosine 5'-phosphate N-glycosylase/hydrolase
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.26 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
DepositionJul 6, 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

Downloads & links

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Assembly

Deposited unit
A: Queuosine salvage protein
B: Queuosine salvage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2784
Polymers78,7242
Non-polymers5552
Water3,495194
1
A: Queuosine salvage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6392
Polymers39,3621
Non-polymers2771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Queuosine salvage protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6392
Polymers39,3621
Non-polymers2771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.726, 136.759, 52.606
Angle α, β, γ (deg.)90.000, 90.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Queuosine salvage protein


Mass: 39361.777 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C9orf64 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q5T6V5
#2: Chemical ChemComp-QEI / 2-amino-5-({[(1S,4S,5R)-4,5-dihydroxycyclopent-2-en-1-yl]amino}methyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / queuine


Mass: 277.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.95 Å3/Da / Density % sol: 37 % / Description: Long, thin clustered crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2M NaCl, 25% PEG3350, 0.1M Bis-Tris, pH 5.5

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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: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.25→45 Å / Num. obs: 27661 / % possible obs: 97.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.226 / Rpim(I) all: 0.095 / Rrim(I) all: 0.245 / Χ2: 0.905 / Net I/σ(I): 4.1 / Num. measured all: 180879
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.295.21.51613040.4780.7051.6781.1794.5
2.29-2.335.81.12213810.6520.51.2320.73197
2.33-2.386.40.86114100.7420.3690.9390.7198.9
2.38-2.426.40.8213710.7420.3490.8920.74498.9
2.42-2.486.50.74213770.8320.3130.8070.7798.4
2.48-2.536.50.68313840.8190.2890.7430.76298.2
2.53-2.66.50.57913910.8590.2440.6290.81998
2.6-2.676.30.5813840.7980.2510.6331.19898.3
2.67-2.756.40.49813650.9070.2130.5430.87797.2
2.75-2.836.10.40113520.9240.1740.4380.88895.1
2.83-2.9470.3613980.9410.1460.3890.90599.1
2.94-3.0570.32914110.950.1340.3550.90899
3.05-3.196.90.26813650.9590.1090.290.93898.5
3.19-3.3670.21713910.9760.0880.2350.99798.3
3.36-3.576.60.19813910.9950.0850.2161.26697.7
3.57-3.856.60.16313750.9780.0680.1771.16197.2
3.85-4.2370.1414150.9820.0580.1521.10699.4
4.23-4.8570.10713890.9910.0430.1160.84999
4.85-6.16.70.10513880.9930.0440.1140.72896.7
6.1-456.90.07714190.9960.0320.0840.61798.3

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Processing

Software
NameVersionClassification
HKL-3000v721.3data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
HKL-3000v721.3data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 7UGK

7ugk


Resolution: 2.26→42.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / SU B: 17.79 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 1234 4.7 %RANDOM
Rwork0.1556 ---
obs0.1587 24766 91.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.67 Å2 / Biso mean: 31.754 Å2 / Biso min: 17.15 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20.38 Å2
2---1.07 Å20 Å2
3----0.18 Å2
Refinement stepCycle: final / Resolution: 2.26→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 40 194 5734
Biso mean--35.78 37.63 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0145862
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175224
X-RAY DIFFRACTIONr_angle_refined_deg1.2051.6577965
X-RAY DIFFRACTIONr_angle_other_deg0.8631.64412273
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70721.45331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.598151041
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8441549
X-RAY DIFFRACTIONr_chiral_restr0.0580.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026731
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021147
X-RAY DIFFRACTIONr_rigid_bond_restr1.227311086
X-RAY DIFFRACTIONr_sphericity_free36.456588
X-RAY DIFFRACTIONr_sphericity_bonded14.465511045
LS refinement shellResolution: 2.26→2.314 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3 46 -
Rwork0.232 1063 -
obs--52.96 %

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