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- PDB-5w6x: Crystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose -

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Basic information

Entry
Database: PDB / ID: 5w6x
TitleCrystal structure of the HsNUDT16 in complex with Mg+2 and ADP-ribose
ComponentsU8 snoRNA-decapping enzyme
KeywordsHYDROLASE / nudix / nudix hydrolase / decapping enzyme / demodification of parylation / marylation
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 / dITP diphosphatase activity / phosphodiesterase decapping endonuclease 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 / dITP diphosphatase activity / phosphodiesterase decapping endonuclease 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 / chloride ion binding / snoRNA binding / cobalt ion binding / mRNA catabolic process / manganese ion binding / mRNA binding / nucleotide 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
ACETIC ACID / ADENOSINE-5-DIPHOSPHORIBOSE / DI(HYDROXYETHYL)ETHER / U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.2Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)44,10311
Polymers42,6612
Non-polymers1,4429
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-73 kcal/mol
Surface area15390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.755, 46.319, 74.238
Angle α, β, γ (deg.)90.000, 107.650, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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: 21330.424 Da / Num. of mol.: 2 / Mutation: A22V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: 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, 275 molecules

#2: Chemical ChemComp-APR / ADENOSINE-5-DIPHOSPHORIBOSE


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.19 Å3/Da / Density % sol: 43.76 % / Mosaicity: 0.838 ° / Mosaicity esd: 0.011 °
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: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 20264 / % possible obs: 92.5 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.076 / Χ2: 2.889 / Net I/σ(I): 14.4 / Num. measured all: 64178
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1820.21412692.04159.1
2.18-2.262.10.20516812.259177.1
2.26-2.372.60.1920632.333194.3
2.37-2.493.40.17521652.622199.8
2.49-2.653.60.14621772.713199.7
2.65-2.853.50.12421572.907199.6
2.85-3.143.50.09421792.976199.4
3.14-3.593.50.06421903.231198.9
3.59-4.523.40.05521633.287198.5
4.52-503.40.05422203.255197.5

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
Cootmodel building
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid XX

Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.2377 / WRfactor Rwork: 0.1808 / FOM work R set: 0.852 / SU B: 4.873 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2725 / SU Rfree: 0.2105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 961 4.8 %RANDOM
Rwork0.1808 ---
obs0.1834 19245 92.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.49 Å2 / Biso mean: 31.301 Å2 / Biso min: 12.53 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å2-0.43 Å2
2--0.76 Å20 Å2
3---0.44 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2751 0 91 266 3108
Biso mean--47.18 35.07 -
Num. residues----353
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192935
X-RAY DIFFRACTIONr_bond_other_d0.0020.022827
X-RAY DIFFRACTIONr_angle_refined_deg1.8672.0183971
X-RAY DIFFRACTIONr_angle_other_deg1.0736456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395358
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48621.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.5115478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7681541
X-RAY DIFFRACTIONr_chiral_restr0.1020.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023291
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02716
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 41 -
Rwork0.19 867 -
all-908 -
obs--58.09 %

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