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- PDB-7uk3: Crystal structure of queuine salvage enzyme DUF2419, wild-type (n... -

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Basic information

Entry
Database: PDB / ID: 7uk3
TitleCrystal structure of queuine salvage enzyme DUF2419, wild-type (non-His6x tagged)
ComponentsQueuosine salvage protein 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 DSM 20745 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 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 31, 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 DUF2419


Theoretical massNumber of molelcules
Total (without water)36,4001
Polymers36,4001
Non-polymers00
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.159, 95.159, 129.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Queuosine salvage protein DUF2419


Mass: 36399.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphaerobacter thermophilus DSM 20745 (bacteria)
Gene: C9orf64 / 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.: 126 / 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: 4.65 Å3/Da / Density % sol: 73.6 % / Description: needle crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2M Sodium thiocynate, 20% PEG3350, pH 6.9

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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, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→42 Å / Num. obs: 30413 / % possible obs: 100 % / Redundancy: 10.3 % / Rmerge(I) obs: 0.265 / Rpim(I) all: 0.086 / Rrim(I) all: 0.279 / Χ2: 0.919 / Net I/σ(I): 3.6 / Num. measured all: 312644
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.349.66.59914790.3092.2256.9710.72199.9
2.34-2.3810.43.53515330.3241.1463.7190.734100
2.38-2.4310.43.06815050.4180.9933.2270.737100
2.43-2.4810.62.59814660.4780.8332.730.731100
2.48-2.5310.42.2314850.5860.7182.3440.751100
2.53-2.5910.31.86615280.5960.6031.9630.73999.9
2.59-2.6610.11.5414840.7220.5051.6220.74999.9
2.66-2.7310.11.28615130.7360.4211.3540.771100
2.73-2.819.10.9515140.7940.3311.0070.815100
2.81-2.910.30.9114920.8610.2950.9570.865100
2.9-310.80.6215180.9120.1960.6510.878100
3-3.1210.70.5115010.9360.1620.5360.88100
3.12-3.2610.70.36415260.9570.1150.3821.02399.9
3.26-3.4410.60.26515190.9760.0840.2781.211100
3.44-3.659.60.20515270.9820.0690.2171.14499.9
3.65-3.9310.70.17415210.9890.0550.1831.207100
3.93-4.33110.14415390.9920.0450.1511.25100
4.33-4.9510.60.11515400.9950.0360.121.258100
4.95-6.249.90.10115630.9950.0340.1070.98699.9
6.24-429.90.06716600.9980.0220.070.83499.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000v721.3data scaling
PDB_EXTRACT3.27data extraction
HKL-3000v721.3data reduction
PHENIXv1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U07

7u07


Resolution: 2.31→41.24 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1746 / WRfactor Rwork: 0.1505 / FOM work R set: 0.8901 / SU B: 10.756 / SU ML: 0.101 / SU Rfree: 0.1452 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1746 1317 5.1 %RANDOM
Rwork0.1505 ---
obs0.1518 24343 84.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.85 Å2 / Biso mean: 38.493 Å2 / Biso min: 18.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å2-0.57 Å20 Å2
2---1.14 Å2-0 Å2
3---3.7 Å2
Refinement stepCycle: final / Resolution: 2.31→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 0 127 2657
Biso mean---38.49 -
Num. residues----319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0142670
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172323
X-RAY DIFFRACTIONr_angle_refined_deg1.0211.6493651
X-RAY DIFFRACTIONr_angle_other_deg0.7831.6275417
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4475332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4619.882170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15515402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1061532
X-RAY DIFFRACTIONr_chiral_restr0.0410.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
X-RAY DIFFRACTIONr_rigid_bond_restr1.48334993
X-RAY DIFFRACTIONr_sphericity_free43.912572
X-RAY DIFFRACTIONr_sphericity_bonded22.85554975
LS refinement shellResolution: 2.31→2.368 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.416 13 -
Rwork0.282 460 -
obs--21.42 %

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