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- PDB-7ugk: Crystal structure of the human queuine salvage enzyme DUF2419, wi... -

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Basic information

Entry
Database: PDB / ID: 7ugk
TitleCrystal structure of the human queuine salvage enzyme DUF2419, wild-type apo form
ComponentsQueuosine salvage protein DUF2419
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 / Queuosine 5'-phosphate N-glycosylase/hydrolase
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 24, 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
B: Queuosine salvage protein DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,1424
Polymers78,7242
Non-polymers4182
Water5,477304
1
A: Queuosine salvage protein DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5712
Polymers39,3621
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Queuosine salvage protein DUF2419
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5712
Polymers39,3621
Non-polymers2091
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.689, 137.513, 52.804
Angle α, β, γ (deg.)90.000, 90.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Queuosine salvage protein DUF2419


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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.02 Å3/Da / Density % sol: 37.52 % / Description: Long, thin clustered crystals
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: Mar 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. obs: 56376 / % possible obs: 96.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Χ2: 0.945 / Net I/σ(I): 9.2 / Num. measured all: 371082
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.78-1.8160.55825190.8160.2450.6120.92588.1
1.81-1.846.60.46328900.8830.1950.5030.91598.2
1.84-1.886.60.4128500.9120.1710.4450.92198.1
1.88-1.926.60.35528080.9350.1490.3860.94897.9
1.92-1.966.60.29128670.9550.1220.3170.96197.4
1.96-26.40.26127690.9590.1110.2840.96996.5
2-2.0560.22427490.9690.0980.2460.99693.7
2.05-2.116.60.19528220.9790.0810.2111.00296.9
2.11-2.176.70.15828300.9830.0660.1720.98198.8
2.17-2.246.80.13829050.9880.0570.1490.99298.6
2.24-2.326.60.12228200.990.0510.1331.01197.4
2.32-2.426.50.10528210.9920.0440.1140.96196.6
2.42-2.536.10.09127460.9930.0390.10.96393.5
2.53-2.666.80.07928660.9950.0320.0850.94499
2.66-2.836.80.06928560.9960.0280.0750.94698.2
2.83-3.046.80.05728490.9970.0230.0620.90897.7
3.04-3.356.40.04927840.9980.020.0530.96895.3
3.35-3.8370.04129030.9980.0170.0440.91899.2
3.83-4.836.60.03528130.9980.0150.0380.86495.7
4.83-506.90.03529090.9990.0140.0380.83398.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000v721.3data scaling
PDB_EXTRACT3.27data extraction
HKL-3000v721.3data reduction
PHASERphenix v1.19.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7U07

7u07


Resolution: 1.78→49.34 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.1603 / WRfactor Rwork: 0.1317 / FOM work R set: 0.9393 / SU B: 3.329 / SU ML: 0.05 / SU Rfree: 0.0986 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1603 2837 5 %RANDOM
Rwork0.1318 ---
obs0.1332 53371 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.5 Å2 / Biso mean: 20.888 Å2 / Biso min: 9.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0 Å2-0.1 Å2
2--0.03 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.78→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 28 306 5834
Biso mean--27.81 29.58 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0135855
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155511
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.6377947
X-RAY DIFFRACTIONr_angle_other_deg1.3911.58212714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8535735
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.89221.287334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.732151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9131551
X-RAY DIFFRACTIONr_chiral_restr0.0730.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026691
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021407
X-RAY DIFFRACTIONr_rigid_bond_restr1.459311366
LS refinement shellResolution: 1.781→1.827 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.172 174 -
Rwork0.081 3806 -
all-3980 -
obs--92.6 %

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