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- PDB-2xsq: Crystal structure of human Nudix motif 16 (NUDT16) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2xsq
TitleCrystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium
ComponentsU8 SNORNA-DECAPPING ENZYME
KeywordsHYDROLASE / MRNA DECAPPING / MRNA TURNOVER / STRUCTURAL GENOMICS CONSORTIUM / SGC
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 / negative regulation of rRNA processing / phosphodiesterase decapping endonuclease activity ...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 / negative regulation of rRNA processing / phosphodiesterase decapping endonuclease activity / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / NAD-cap decapping / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Phosphate bond hydrolysis by NUDT proteins / metalloexopeptidase activity / chloride ion binding / cobalt 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
: / U8 snoRNA-decapping enzyme-like / 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
INOSINIC ACID / U8 snoRNA-decapping enzyme
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van den Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P.
CitationJournal: Plos One / Year: 2015
Title: Structural Basis for the Specificity of Human Nudt16 and its Regulation by Inosine Monophosphate.
Authors: Tresaugues, L. / Lundback, T. / Welin, M. / Flodin, S. / Nyman, T. / Silvander, C. / Graslund, S. / Nordlund, P.
History
DepositionSep 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references / Version format compliance
Revision 1.2Dec 13, 2017Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U8 SNORNA-DECAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3215
Polymers23,8891
Non-polymers4324
Water4,252236
1
A: U8 SNORNA-DECAPPING ENZYME
hetero molecules

A: U8 SNORNA-DECAPPING ENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,64310
Polymers47,7782
Non-polymers8658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area4640 Å2
ΔGint-68.9 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.583, 141.583, 141.583
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number196
Space group name H-MF23
Components on special symmetry positions
IDModelComponents
11A-2060-

HOH

21A-2175-

HOH

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Components

#1: Protein U8 SNORNA-DECAPPING ENZYME / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 16 / U8 SNORNA-BINDING PROTEIN H29K / NUDIX MOTIF 16


Mass: 23889.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)R3 PRARE
References: UniProt: Q96DE0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.48 Å3/Da / Density % sol: 50.41 % / Description: NONE
Crystal growpH: 7.5
Details: PROTEIN WAS MIXED WITH 5MM MGCL2 AND 2MM IDP PRIOR SETTING-UP THE PLATES. THEN IT WAS CRYSTALLIZED FROM 20MM MGCL2, 22% W/V POLYACRYLIC ACID 5100 AND 0.1M HEPES PH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 8, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.72→42.69 Å / Num. obs: 25010 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 21.062 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3COU

3cou


Resolution: 1.72→81.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.627 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18145 1273 5.1 %RANDOM
Rwork0.15864 ---
obs0.15983 23737 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.756 Å2
Refinement stepCycle: LAST / Resolution: 1.72→81.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1393 0 26 236 1655
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211476
X-RAY DIFFRACTIONr_bond_other_d0.0010.021037
X-RAY DIFFRACTIONr_angle_refined_deg1.2762.0062004
X-RAY DIFFRACTIONr_angle_other_deg0.83832492
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5535188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.12921.80672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.18415246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5961520
X-RAY DIFFRACTIONr_chiral_restr0.0670.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211666
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6661.5895
X-RAY DIFFRACTIONr_mcbond_other0.1331.5376
X-RAY DIFFRACTIONr_mcangle_it1.26921420
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9463581
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3224.5579
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.72→1.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 82 -
Rwork0.296 1765 -
obs--100 %

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