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- PDB-5lf8: Human Nucleoside diphosphate-linked moiety X motif 17 (NUDT17) -

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Basic information

Entry
Database: PDB / ID: 5lf8
TitleHuman Nucleoside diphosphate-linked moiety X motif 17 (NUDT17)
ComponentsNucleoside diphosphate-linked moiety X motif 17
KeywordsHYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


NADP+ catabolic process / NADH pyrophosphatase activity / NAD+ catabolic process / : / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisome / metal ion binding
Similarity search - Function
Nudix motif 17 domain / : / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
ETHYL MERCURY ION / PHOSPHATE ION / Nucleoside diphosphate-linked moiety X motif 17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.56 Å
AuthorsMathea, S. / Tallant, C. / Salah, E. / Wang, D. / Velupillai, S. / Nowak, R. / Oerum, S. / Krojer, T. / Burgess-Brown, N. / von Delft, F. ...Mathea, S. / Tallant, C. / Salah, E. / Wang, D. / Velupillai, S. / Nowak, R. / Oerum, S. / Krojer, T. / Burgess-Brown, N. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Huber, K. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Human Nucleoside diphosphate-linked moiety X motif 17 (NUDT17)
Authors: Huber, K.
History
DepositionJun 30, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate-linked moiety X motif 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5174
Polymers35,9621
Non-polymers5543
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-11 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.913, 151.913, 81.495
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Nucleoside diphosphate-linked moiety X motif 17 / Nudix motif 17


Mass: 35962.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT17 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0C025, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5Hg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M SPG pH 7.0 30% PEG1K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.56→75.96 Å / Num. obs: 11806 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 18
Reflection shellHighest resolution: 2.56 Å

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Processing

Software
NameVersionClassification
REFMAC5.7refinement
xia2data reduction
xia2data scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.56→75.96 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.9 / SU B: 14.873 / SU ML: 0.305 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.31 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29823 621 5.3 %RANDOM
Rwork0.2272 ---
obs0.23072 11183 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 69.608 Å2
Baniso -1Baniso -2Baniso -3
1--3.26 Å2-1.63 Å2-0 Å2
2---3.26 Å2-0 Å2
3---10.56 Å2
Refinement stepCycle: 1 / Resolution: 2.56→75.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1770 0 11 3 1784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191822
X-RAY DIFFRACTIONr_bond_other_d0.0020.021670
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9782503
X-RAY DIFFRACTIONr_angle_other_deg0.98933794
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0565246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85222.24549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.3215220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.109159
X-RAY DIFFRACTIONr_chiral_restr0.0810.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212033
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
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_it5.7997.5691005
X-RAY DIFFRACTIONr_mcbond_other5.87.5691004
X-RAY DIFFRACTIONr_mcangle_it8.5411.3291244
X-RAY DIFFRACTIONr_mcangle_other8.53811.3291245
X-RAY DIFFRACTIONr_scbond_it5.4517.631817
X-RAY DIFFRACTIONr_scbond_other5.4297.63817
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.96411.3691260
X-RAY DIFFRACTIONr_long_range_B_refined11.34361.0641874
X-RAY DIFFRACTIONr_long_range_B_other11.3461.0691875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.555→2.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.465 41 -
Rwork0.442 826 -
obs--99.88 %

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