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- PDB-5w6z: Crystal structure of the H24W mutant of HsNUDT16 -

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Basic information

Entry
Database: PDB / ID: 5w6z
TitleCrystal structure of the H24W mutant of HsNUDT16
ComponentsU8 snoRNA-decapping enzyme
KeywordsHYDROLASE / nudix / nudix hydrolase / decapping enzyme / demodification of parylation
Function / homology
Function and homology information


inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing / NAD-cap decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Phosphate bond hydrolysis by NUDT proteins / metalloexopeptidase activity / cobalt ion binding / chloride ion binding / snoRNA binding / mRNA catabolic process / manganese ion binding / nucleotide binding / mRNA binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsThirawatananond, P. / Gabelli, S.B.
Funding support United States, 2items
OrganizationGrant numberCountry
Allegheny Health Network United States
DoD-CDMRP United States
CitationJournal: Sci Rep / Year: 2019
Title: Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(ADP-ribosyl)ated proteins.
Authors: Thirawatananond, P. / McPherson, R.L. / Malhi, J. / Nathan, S. / Lambrecht, M.J. / Brichacek, M. / Hergenrother, P.J. / Leung, A.K.L. / Gabelli, S.B.
History
DepositionJun 18, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: U8 snoRNA-decapping enzyme
B: U8 snoRNA-decapping enzyme
D: U8 snoRNA-decapping enzyme
E: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,5375
Polymers85,5144
Non-polymers231
Water1,20767
1
A: U8 snoRNA-decapping enzyme
B: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7803
Polymers42,7572
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-29 kcal/mol
Surface area16160 Å2
MethodPISA
2
D: U8 snoRNA-decapping enzyme
E: U8 snoRNA-decapping enzyme


Theoretical massNumber of molelcules
Total (without water)42,7572
Polymers42,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-16 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.117, 119.438, 65.777
Angle α, β, γ (deg.)90.000, 90.690, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
U8 snoRNA-decapping enzyme / IDP phosphatase / IDPase / Inosine diphosphate phosphatase / Nucleoside diphosphate-linked moiety X ...IDP phosphatase / IDPase / Inosine diphosphate phosphatase / Nucleoside diphosphate-linked moiety X motif 16 / Nudix motif 16 / Nudix hydrolase 16 / U8 snoRNA-binding protein H29K / m7GpppN-mRNA hydrolase


Mass: 21378.486 Da / Num. of mol.: 4 / Mutation: A22V, H24W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) codon plus RIPL
References: UniProt: Q96DE0, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, inosine diphosphate phosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.31 Å3/Da / Density % sol: 46.76 % / Mosaicity: 0.568 ° / Mosaicity esd: 0.008 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5 / Details: PEG 8000, CHES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 21134 / % possible obs: 90.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.083 / Rrim(I) all: 0.15 / Χ2: 2.605 / Net I/σ(I): 8 / Num. measured all: 64806
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.642.40.2610.9190.1890.3241.03352.4
2.64-2.692.50.2690.8930.1920.3320.97756.5
2.69-2.742.60.2650.870.1880.3271.03165.4
2.74-2.82.80.2470.9020.1710.3021.03773.2
2.8-2.862.80.2470.9020.1670.31.0683.9
2.86-2.9330.2350.9170.1580.2851.28797.2
2.93-33.30.2320.9290.1490.2771.49599.2
3-3.083.30.2020.9490.1290.241.76199.2
3.08-3.173.30.1860.9540.120.2221.88899.2
3.17-3.283.20.1760.9460.1150.2112.32699.7
3.28-3.3930.150.9560.1030.1822.86199.1
3.39-3.533.20.1450.9710.0960.1743.01398.6
3.53-3.693.30.1450.9650.0940.1733.35998.9
3.69-3.883.20.1340.970.0890.1623.60798.7
3.88-4.1330.1140.9740.0780.1383.93597.9
4.13-4.4530.1070.9740.0750.1314.01896.7
4.45-4.893.20.1030.9790.0690.1244.09297.4
4.89-5.63.10.0980.9770.0660.1183.37498.4
5.6-7.053.30.0920.9820.060.112.96199.2
7.05-502.90.0710.9920.050.0883.52790.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W6X

5w6x


Resolution: 2.61→50 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.84 / SU B: 16.157 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.446
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3032 1047 5 %RANDOM
Rwork0.2082 ---
obs0.2131 20067 89.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.68 Å2 / Biso mean: 45.342 Å2 / Biso min: 13.48 Å2
Baniso -1Baniso -2Baniso -3
1--3.07 Å20 Å2-0.1 Å2
2--4.52 Å20 Å2
3----1.44 Å2
Refinement stepCycle: final / Resolution: 2.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5562 0 1 67 5630
Biso mean--30 31.46 -
Num. residues----713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195774
X-RAY DIFFRACTIONr_bond_other_d0.0020.025621
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.9847820
X-RAY DIFFRACTIONr_angle_other_deg1.052312842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73521.761284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15315970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7531579
X-RAY DIFFRACTIONr_chiral_restr0.0940.2849
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216635
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021420
LS refinement shellResolution: 2.611→2.678 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 30 -
Rwork0.289 817 -
all-847 -
obs--48.96 %

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