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- PDB-3gg6: Crystal structure of the NUDIX domain of human NUDT18 -

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Basic information

Entry
Database: PDB / ID: 3gg6
TitleCrystal structure of the NUDIX domain of human NUDT18
ComponentsNucleoside diphosphate-linked moiety X motif 18
KeywordsHYDROLASE / NUDIX / NUDT18 / NXR1 / NUCLEOTIDE HYDROLASE / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / SGC STOCKHOLM / Alternative splicing / Magnesium / Manganese / Metal-binding
Function / homology
Function and homology information


8-hydroxy-dADP phosphatase activity / dADP catabolic process / GDP catabolic process / dGDP catabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / magnesium ion binding / cytosol
Similarity search - Function
NUDT18, NUDIX hydrolase domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily ...NUDT18, NUDIX hydrolase domain / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / 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
8-oxo-dGDP phosphatase NUDT18
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTresaugues, L. / Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. ...Tresaugues, L. / Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the NUDIX domain of human NUDT18
Authors: Tresaugues, L. / Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / ...Authors: Tresaugues, L. / Siponen, M.I. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Dahlgren, L.G. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, A. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E. / Nyman, T. / Persson, C. / Sagemark, J. / Schueler, H. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Wisniewska, M. / Nordlund, P.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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: Nucleoside diphosphate-linked moiety X motif 18


Theoretical massNumber of molelcules
Total (without water)17,5011
Polymers17,5011
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.660, 60.130, 76.090
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 Nucleoside diphosphate-linked moiety X motif 18 / Nudix motif 18


Mass: 17501.084 Da / Num. of mol.: 1 / Fragment: Nudix hydrolase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT18 / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q6ZVK8, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / pH: 5.5
Details: Tri-sodium citrate dihydrate 0.1M pH 5.5, PEG3000 20% w/v, 2mM 2 deoxyguanosine, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98003
DetectorType: ADSC QUANTUM Q315r / Detector: CCD / Date: Dec 11, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98003 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. obs: 8985 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.88 % / Biso Wilson estimate: 15.99 Å2 / Rmerge(I) obs: 0.161
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 5.22 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 4.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2B0V

2b0v


Resolution: 2.1→21.801 Å / SU ML: 0.12 / σ(F): 2 / Phase error: 19.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2256 897 10.03 %
Rwork0.1636 --
obs0.1699 8945 99.93 %
all-8945 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.688 Å2 / ksol: 0.425 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→21.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1168 0 0 133 1301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0221197
X-RAY DIFFRACTIONf_angle_d1.8161631
X-RAY DIFFRACTIONf_dihedral_angle_d17.226454
X-RAY DIFFRACTIONf_chiral_restr0.117184
X-RAY DIFFRACTIONf_plane_restr0.009211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.23150.24871450.16851304X-RAY DIFFRACTION100
2.2315-2.40350.24991450.15991311X-RAY DIFFRACTION100
2.4035-2.64510.23771480.16091330X-RAY DIFFRACTION100
2.6451-3.02690.21071480.15531326X-RAY DIFFRACTION100
3.0269-3.81030.23081510.14811352X-RAY DIFFRACTION100
3.8103-21.80240.18931600.17121425X-RAY DIFFRACTION100

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