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- PDB-6b09: Crystal structure of HsNUDT16 in complex with diADPR (soaked) -

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Basic information

Entry
Database: PDB / ID: 6b09
TitleCrystal structure of HsNUDT16 in complex with diADPR (soaked)
ComponentsU8 snoRNA-decapping enzyme
KeywordsHYDROLASE / nudix hydrolase / decapping enzyme / demodification of parylation / hydrolase
Function / homologyNUDIX hydrolase-like domain superfamily / NUDIX hydrolase domain / Phosphate bond hydrolysis by NUDT proteins / Nudix hydrolase domain profile. / NUDIX domain / IDP phosphatase activity / dIDP diphosphatase activity / inosine diphosphate phosphatase / snoRNA catabolic process / XTP binding ...NUDIX hydrolase-like domain superfamily / NUDIX hydrolase domain / Phosphate bond hydrolysis by NUDT proteins / Nudix hydrolase domain profile. / NUDIX domain / IDP phosphatase activity / dIDP diphosphatase activity / inosine diphosphate phosphatase / snoRNA catabolic process / XTP binding / XDP catabolic process / ITP binding / phosphodiesterase decapping endonuclease activity / IDP catabolic process / negative regulation of rRNA processing / dITP catabolic process / positive regulation of cell cycle process / nucleotide phosphatase activity, acting on free nucleotides / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / dITP diphosphatase activity / positive regulation of double-strand break repair / m7G(5')pppN diphosphatase activity / adenosine to inosine editing / nucleobase-containing small molecule catabolic process / RNA phosphodiester bond hydrolysis, endonucleolytic / metalloexopeptidase activity / snoRNA binding / mRNA catabolic process / cobalt ion binding / chloride ion binding / manganese ion binding / mRNA binding / GTP binding / nucleolus / positive regulation of cell population proliferation / magnesium ion binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm / U8 snoRNA-decapping enzyme
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 3.2 Å resolution
AuthorsThirawatananond, P. / Gabelli, S.B.
CitationJournal: Sci Rep / Year: 2019
Title: Structural analyses of NudT16-ADP-ribose complexes direct rational design of mutants with improved processing of poly(AD-ribosyl)ated proteins
Authors: Thirawatananond, P. / McPherson, R.L. / Malhi, J. / Nathan, S. / Lambrecht, M. / Brichacek, M. / Hergenrother, P. / Leung, A. / Gabelli, S.B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 14, 2017 / Release: Jan 9, 2019

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,77711
Polyers42,6612
Non-polymers2,1169
Water543
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)3810
ΔGint (kcal/M)-73
Surface area (Å2)16090
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)113.395, 47.063, 75.792
Angle α, β, γ (deg.)90.000, 108.740, 90.000
Int Tables number5
Space group name H-MC 1 2 1

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide U8 snoRNA-decapping enzyme / 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: 21330.424 Da / Num. of mol.: 2 / Mutation: A22V / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid name: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIPL
References: UniProt: Q96DE0, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, inosine diphosphate phosphatase

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Non-polymers , 5 types, 12 molecules

#2: Chemical ChemComp-C7G / [(2~{R},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-[(2~{S},3~{S},4~{S},5~{S})-5-[[[[(2~{R},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate / DIADPR


Mass: 968.502 Da / Num. of mol.: 2 / Formula: C25H36N10O23P4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Formula: Cl / Chloride
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Formula: Na / Sodium
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Formula: H2O / Water

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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: 2.25 / Density percent sol: 45.28 % / Mosaicity: 2.866 deg. / Mosaicity esd: 0.061 deg.
Crystal growTemp: 293 K / Method: vapor diffusion / pH: 9.5 / Details: PEG 8000, CHES

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Data collection

DiffractionMean temperature: 100 kelvins / Serial crystal experiment: N
SourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5417 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Collection date: Dec 17, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionD resolution high: 3.2 Å / D resolution low: 6 Å / Number obs: 6140 / Rmerge I obs: 0.167 / Rpim I all: 0.131 / Rrim I all: 0.214 / Chi squared: 1.856 / NetI over sigmaI: 6 / Number measured all: 13751 / Redundancy: 2.2 % / Percent possible obs: 91.4
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionNumber unique obsCC halfRpim I allRrim I allChi squaredRedundancyPercent possible all
0.5923.2003.2603200.5100.4690.7591.2572.10095.500
0.4353.2603.3103190.6840.3380.5531.1572.20095.800
0.2883.3103.3803140.6880.2220.3661.1032.30095.700
0.2473.3803.4503090.7490.1920.3151.3442.30093.600
0.2773.4503.5203110.8170.2180.3541.4262.30095.700
0.3083.5203.6003270.8050.2430.3941.3432.30095.900
0.5983.6003.6903080.8370.4920.7791.5862.10090.900
0.3283.6903.7902800.8300.2600.4212.8622.30089.500
0.1593.7903.9103070.8290.1240.2023.3132.30089.500
0.3913.9104.0302890.8860.3110.5022.4902.20089.200
0.1694.0304.1803230.9570.1310.2151.4332.30092.600
0.1594.1804.3402980.9660.1220.2011.5112.40091.400
0.1404.3404.5402900.9740.1070.1782.1442.10085.800
0.1164.5404.7802740.9470.0950.1513.2272.10081.800
0.1334.7805.0802990.9740.1050.1701.8562.20089.300
0.1285.0805.4703120.9730.0960.1611.5622.40093.100
0.1215.4706.0203210.9700.0950.1551.5892.30093.600
0.1216.0206.8903150.9720.0930.1541.7342.30092.600
0.0796.8908.6803090.9850.0630.1021.9882.20090.900
0.0498.68060.0003150.9910.0410.0643.0162.00085.800

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Processing

Software
NameVersionClassification
REFMACrefinement
StructureStudiodata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
HKL-3000data reduction
MOLREPphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Correlation coeff Fo to Fc: 0.857 / Correlation coeff Fo to Fc free: 0.816
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Overall FOM work R set: 0.8293 / Overall SU B: 26.612 / Overall SU ML: 0.445 / Overall SU R free: 0.6745 / R Free selection details: RANDOM / Cross valid method: THROUGHOUT / Sigma F: 0 / Overall ESU R Free: 0.674 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Solvent computationSolvent ion probe radii: 0.8 Å / Solvent shrinkage radii: 0.8 Å / Solvent vdw probe radii: 1.2 Å / Solvent model details: MASK
Displacement parametersB iso max: 185.06 Å2 / B iso mean: 50.797 Å2 / B iso min: 12.44 Å2 / Aniso B11: -5.21 Å2 / Aniso B12: 0 Å2 / Aniso B13: 1.58 Å2 / Aniso B22: -2.15 Å2 / Aniso B23: 0 Å2 / Aniso B33: 5.11 Å2
Least-squares processR factor R free: 0.2791 / R factor R work: 0.2555 / R factor obs: 0.2566 / Highest resolution: 3.2 Å / Lowest resolution: 37.62 Å / Number reflection R free: 283 / Number reflection obs: 5564 / Percent reflection R free: 4.8 / Percent reflection obs: 90.82 / WR factor R free: 0.2791 / WR factor R work: 0.2555
Refine hist #finalHighest resolution: 3.2 Å / Lowest resolution: 37.62 Å / B iso mean ligand: 73.03 / B iso mean solvent: 26.1 / Number residues total: 351
Number of atoms included #finalProtein: 2740 / Nucleic acid: 0 / Ligand: 131 / Solvent: 3 / Total: 2874
Refine LS restraints
Refine IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0100.0132929
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172743
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.7133977
X-RAY DIFFRACTIONr_angle_other_deg1.4641.6056289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7725.000347
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.81819.080174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.47915.000466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.26215.00038
X-RAY DIFFRACTIONr_chiral_restr0.0900.200353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0203238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.020700
Refine LS shellHighest resolution: 3.2 Å / R factor R free: 0.299 / R factor R free error: 0 / R factor R work: 0.262 / Lowest resolution: 3.283 Å / Number reflection R free: 24 / Number reflection R work: 432 / Number reflection all: 456 / Total number of bins used: 20 / Percent reflection obs: 95.8

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