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- PDB-3mgm: Crystal structure of human NUDT16 -

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Basic information

Entry
Database: PDB / ID: 3mgm
TitleCrystal structure of human NUDT16
ComponentsU8 snoRNA-decapping enzyme
KeywordsHYDROLASE / hNUDT16 / Nudix fold / two domains / dimmer
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 / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsYan, J. / Lu, G. / Zhang, J. / Qi, J. / Li, Z. / Gao, F.
CitationJournal: To be Published
Title: Crystal structure and the template mRNA decapping activity of human NUDT16
Authors: Lu, G. / Zhang, J. / Li, Z. / Zhang, Q. / Qi, J. / Gao, F. / Peng, H. / Wang, T. / Gao, G.F. / Yan, J.
History
DepositionApr 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)43,9722
Polymers43,9722
Non-polymers00
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-16 kcal/mol
Surface area15170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.412, 79.153, 97.422
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein U8 snoRNA-decapping enzyme / Nucleoside diphosphate-linked moiety X motif 16 / Nudix motif 16 / U8 snoRNA-binding protein H29K


Mass: 21986.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: hNUDT16, NUDT16 / Plasmid: pET-30a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96DE0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 32018 / Num. obs: 32018 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 39.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 7.75 / Num. unique all: 230397 / Rsym value: 0.323 / % possible all: 96.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1U20

1u20


Resolution: 1.801→24.355 Å / SU ML: 0.2 / σ(F): 0.1 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 1589 5.04 %
Rwork0.1839 --
obs0.1847 31528 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.09 Å2 / ksol: 0.355 e/Å3
Refinement stepCycle: LAST / Resolution: 1.801→24.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2554 0 0 367 2921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042610
X-RAY DIFFRACTIONf_angle_d0.8623526
X-RAY DIFFRACTIONf_dihedral_angle_d16.016956
X-RAY DIFFRACTIONf_chiral_restr0.06384
X-RAY DIFFRACTIONf_plane_restr0.003466
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8008-1.85890.23711350.1803252491
1.8589-1.92530.22891510.1662255993
1.9253-2.00230.19891240.1589263496
2.0023-2.09340.19051270.1643269696
2.0934-2.20370.20591400.1596269997
2.2037-2.34170.20261610.1701268197
2.3417-2.52230.22681430.1812273898
2.5223-2.77580.21981430.18279399
2.7758-3.17670.21161490.1916280099
3.1767-3.99950.15121490.17172846100
3.9995-24.35770.19231670.19312969100
Refinement TLS params.Method: refined / Origin x: 2.1706 Å / Origin y: 2.1127 Å / Origin z: 3.5338 Å
111213212223313233
T0.0948 Å2-0.0025 Å20.0042 Å2-0.0943 Å20.0041 Å2--0.1214 Å2
L0.4481 °2-0.0276 °20.0715 °2-0.6419 °20.0161 °2--1.0648 °2
S0.0065 Å °-0.0323 Å °-0.031 Å °0.0367 Å °-0.0122 Å °0.0548 Å °0.0339 Å °-0.0765 Å °0 Å °
Refinement TLS groupSelection details: all

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