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- PDB-6x7u: Crystal Structure of the Human Nudix Hydrolase Nudt16 in complex ... -

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Basic information

Entry
Database: PDB / ID: 6x7u
TitleCrystal Structure of the Human Nudix Hydrolase Nudt16 in complex with FAD
ComponentsU8 snoRNA-decapping enzyme
KeywordsHydrolase / RNA BINDING PROTEIN / Nudix / FAD / Decapping
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
ADENOSINE MONOPHOSPHATE / FLAVIN-ADENINE DINUCLEOTIDE / : / U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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.pdbx_dist_value / _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

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Assembly

Deposited unit
A: U8 snoRNA-decapping enzyme
C: U8 snoRNA-decapping enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,6698
Polymers40,3162
Non-polymers1,3536
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-48 kcal/mol
Surface area14350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.721, 64.721, 77.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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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: 20158.020 Da / Num. of mol.: 2
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-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium chloride and 20% (w/v) PEG 3350

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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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.644
11K, H, -L20.356
ReflectionResolution: 2.7→45.5 Å / Num. obs: 9929 / % possible obs: 99.5 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.4
Reflection shellResolution: 2.7→2.87 Å / Mean I/σ(I) obs: 1.65 / Num. unique obs: 1602 / CC1/2: 0.602

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3COU

3cou


Resolution: 2.7→45.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.91 / SU B: 11.627 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 448 4.5 %RANDOM
Rwork0.1587 ---
obs0.1619 9480 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 166.41 Å2 / Biso mean: 56.583 Å2 / Biso min: 31.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å20 Å20 Å2
2--2.01 Å20 Å2
3----4.01 Å2
Refinement stepCycle: final / Resolution: 2.7→45.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2524 0 80 36 2640
Biso mean--70.22 48.33 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132657
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172482
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6473602
X-RAY DIFFRACTIONr_angle_other_deg1.1511.5765695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7275321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.83919.255161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.35515425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1611534
X-RAY DIFFRACTIONr_chiral_restr0.0540.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02630
LS refinement shellResolution: 2.703→2.773 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 30 -
Rwork0.395 695 -
all-725 -
obs--99.86 %

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