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- PDB-6x7v: Crystal Structure of the Human Nudix Hydrolase Nudt16 -

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Basic information

Entry
Database: PDB / ID: 6x7v
TitleCrystal Structure of the Human Nudix Hydrolase Nudt16
ComponentsU8 snoRNA-decapping enzyme
KeywordsHydrolase / RNA BINDING PROTEIN / Nudix
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 / molecular replacement / Resolution: 2.3 Å
AuthorsHamilton, K. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Complementary and Integrative Health (NIH/NCCIH)R35GM118093 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs.
Authors: Sharma, S. / Grudzien-Nogalska, E. / Hamilton, K. / Jiao, X. / Yang, J. / Tong, L. / Kiledjian, M.
History
DepositionMay 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 2023Group: 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_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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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
C: U8 snoRNA-decapping enzyme
D: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3006
Polymers85,2094
Non-polymers902
Water97354
1
A: U8 snoRNA-decapping enzyme
B: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6603
Polymers42,6052
Non-polymers551
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-18 kcal/mol
Surface area14190 Å2
MethodPISA
2
C: U8 snoRNA-decapping enzyme
D: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6403
Polymers42,6052
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-24 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.686, 137.922, 54.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 21302.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT16 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q96DE0, 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase, inosine diphosphate phosphatase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.01 Å3/Da / Density % sol: 38.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium chloride, 20% (w/v) PEG 3350, 0.1 M MES pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→46.3 Å / Num. obs: 28854 / % possible obs: 97.6 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Net I/σ(I): 10.5
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.765 / Num. unique obs: 4458 / CC1/2: 0.746 / % possible all: 95.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.77 Å46.28 Å
Translation4.77 Å46.28 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDS20180808data reduction
XDS20180808data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MGM

3mgm


Resolution: 2.3→46.28 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2873 1442 5 %RANDOM
Rwork0.2243 27395 --
obs0.2275 28837 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.61 Å2 / Biso mean: 63.923 Å2 / Biso min: 39.08 Å2
Refinement stepCycle: final / Resolution: 2.3→46.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5030 0 2 54 5086
Biso mean--55.22 54.02 -
Num. residues----642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3-2.390.46291360.376257492
2.39-2.480.36611440.33552740100
2.48-2.60.3361440.2965273999
2.6-2.730.33571440.2784274199
2.73-2.90.36211430.2745272298
2.9-3.130.3691450.2677274899
3.13-3.440.33281450.2399277699
3.44-3.940.29931440.2229272497
3.94-4.960.2281470.172278198
4.96-46.280.24141500.199285095

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