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- PDB-4xp7: Crystal structure of Human tRNA dihydrouridine synthase 2 -

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Basic information

Entry
Database: PDB / ID: 4xp7
TitleCrystal structure of Human tRNA dihydrouridine synthase 2
ComponentstRNA-dihydrouridine(20) synthase [NAD(P)+]-like
KeywordsOXIDOREDUCTASE / tRNA / DUS
Function / homology
Function and homology information


tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / FMN binding ...tRNA-dihydrouridine20 synthase [NAD(P)+] / tRNA-dihydrouridine20 synthase activity / tRNA dihydrouridine synthesis / tRNA dihydrouridine synthase activity / tRNA modification in the nucleus and cytosol / protein kinase inhibitor activity / antiviral innate immune response / NADPH binding / PKR-mediated signaling / FMN binding / double-stranded RNA binding / flavin adenine dinucleotide binding / tRNA binding / endoplasmic reticulum / cytosol / cytoplasm
Similarity search - Function
DUS2, double-stranded RNA binding domain / tRNA-dihydrouridine synthase, conserved site / DUS-like, FMN-binding domain / Dihydrouridine synthase (Dus) / Uncharacterized protein family UPF0034 signature. / Double-stranded RNA binding motif / Double-stranded RNA binding motif / Double-stranded RNA-binding domain / Aldolase-type TIM barrel
Similarity search - Domain/homology
Chem-FNR / tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsWhelan, F. / Jenkins, H.T. / Griffiths, S. / Byrne, R.T. / Dodson, E.J. / Antson, A.A.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust081916 United Kingdom
Wellcome Trust098230 United Kingdom
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: From bacterial to human dihydrouridine synthase: automated structure determination.
Authors: Whelan, F. / Jenkins, H.T. / Griffiths, S.C. / Byrne, R.T. / Dodson, E.J. / Antson, A.A.
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1292
Polymers38,6711
Non-polymers4581
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-6 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.252, 49.562, 69.612
Angle α, β, γ (deg.)90.000, 95.710, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein tRNA-dihydrouridine(20) synthase [NAD(P)+]-like / Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine ...Dihydrouridine synthase 2 / Up-regulated in lung cancer protein 8 / URLC8 / tRNA-dihydrouridine synthase 2-like / hDUS2


Mass: 38670.527 Da / Num. of mol.: 1 / Fragment: UNP residues 1-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUS2, DUS2L / Production host: Escherichia Coli BL21(DE3) (bacteria)
References: UniProt: Q9NX74, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-FNR / 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL / TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE


Mass: 458.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H23N4O9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.13 Å3/Da / Density % sol: 40.2 % / Description: Rod-like clusters that separate readily
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.1 M MES Malic Tris pH 4, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→46.02 Å / Num. all: 24244 / Num. obs: 24244 / % possible obs: 97.6 % / Redundancy: 3 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.075 / Rsym value: 0.063 / Net I/av σ(I): 7.552 / Net I/σ(I): 10.3 / Num. measured all: 72405
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-22.80.5851.3991935150.4140.5851.797.8
2-2.122.90.3172.4968833830.2220.3173.298.9
2.12-2.272.90.1834.2907631440.1280.1835.398.3
2.27-2.452.90.1276.1847629290.0880.1277.397.8
2.45-2.692.90.0849782226970.0580.08410.297.7
2.69-32.90.05612.7702424060.0380.05614.396.9
3-3.472.90.04813610121100.0330.04818.495.2
3.47-4.252.80.04113.8503717790.0280.04122.194.9
4.25-6.014.40.05111.4633814450.0260.05124.998.5
6.01-49.5623.50.03614.429248360.0230.03622.999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation46.02 Å3 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALA3.3.16data scaling
MOLREP11.0.02phasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet model

Resolution: 1.9→46.02 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.096 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1236 5.1 %RANDOM
Rwork0.1679 22995 --
obs0.1699 22995 97.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.29 Å2 / Biso mean: 36.622 Å2 / Biso min: 16.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.12 Å2
2--1.1 Å2-0 Å2
3----0.84 Å2
Refinement stepCycle: final / Resolution: 1.9→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2466 0 31 196 2693
Biso mean--23.17 39.41 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192609
X-RAY DIFFRACTIONr_bond_other_d0.0010.022493
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.973561
X-RAY DIFFRACTIONr_angle_other_deg0.82835710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4623.75112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3921522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02582
X-RAY DIFFRACTIONr_mcbond_it1.4462.3731326
X-RAY DIFFRACTIONr_mcbond_other1.4362.3681325
X-RAY DIFFRACTIONr_mcangle_it2.1183.9831664
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 78 -
Rwork0.305 1674 -
all-1752 -
obs--96.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5436-0.16881.08010.8957-0.60062.62160.06130.4253-0.1124-0.0107-0.0496-0.12350.19960.3868-0.01170.07010.03390.0480.0817-0.01150.078721.289-123.471
25.780.23312.16171.7818-0.40954.3588-0.10630.99250.587-0.4311-0.0745-0.1212-0.20940.43250.18080.2536-0.00370.0910.43420.06170.109620.42424.16574.6777
32.7981-0.7251-0.07961.55540.56935.6347-0.06750.0982-0.0128-0.0610.06480.16950.0485-0.48950.00270.0325-0.02070.02830.06120.00820.07971.97120.505724.7661
49.6382-3.35022.35592.7444-0.73611.3299-0.0024-0.05930.09950.13670.0149-0.13610.0518-0.0944-0.01240.15390.02620.01720.10190.00530.103115.3505-6.833447.2673
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 109
2X-RAY DIFFRACTION2A110 - 220
3X-RAY DIFFRACTION3A221 - 319
4X-RAY DIFFRACTION4A320 - 338

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