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- PDB-3l85: Crystal structure of human NUDT5 complexed with 8-oxo-dGMP -

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Basic information

Entry
Database: PDB / ID: 3l85
TitleCrystal structure of human NUDT5 complexed with 8-oxo-dGMP
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Nudix motif / Magnesium / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / 8-oxo-GDP phosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
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-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.301 Å
AuthorsArimori, T. / Yamagata, Y.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Diverse substrate recognition and hydrolysis mechanisms of human NUDT5
Authors: Arimori, T. / Tamaoki, H. / Nakamura, T. / Kamiya, H. / Ikemizu, S. / Takagi, Y. / Ishibashi, T. / Harashima, H. / Sekiguchi, M. / Yamagata, Y.
History
DepositionDec 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Database references / Structure summary
Revision 1.3Jun 5, 2013Group: Database references
Revision 1.4Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0144
Polymers43,2872
Non-polymers7262
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6040 Å2
ΔGint-50 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.655, 40.008, 98.470
Angle α, β, γ (deg.)90.00, 121.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADP-sugar pyrophosphatase / NUDT5 / Nucleoside diphosphate-linked moiety X motif 5 / Nudix motif 5 / YSA1H


Mass: 21643.592 Da / Num. of mol.: 2 / Fragment: residues 14-208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, HSPC115 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UKK9, ADP-ribose diphosphatase
#2: Chemical ChemComp-8OG / 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE / 8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Sodium Acetate, 0.8M NaH2PO4/1.2M K2HPO4 , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 15339 / Num. obs: 15339 / % possible obs: 90.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 33.77 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.75 / Num. unique all: 1071 / % possible all: 64.9

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DSC

2dsc


Resolution: 2.301→45.523 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.762 / SU ML: 2.04 / σ(F): 0.06 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.261 706 5.02 %RANDOM
Rwork0.215 13351 --
obs0.217 14057 82.97 %-
all-15339 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.467 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 89.03 Å2 / Biso mean: 43.528 Å2 / Biso min: 21.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.849 Å20 Å2-2.184 Å2
2--7.774 Å2-0 Å2
3---2.075 Å2
Refinement stepCycle: LAST / Resolution: 2.301→45.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3034 0 37 75 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033132
X-RAY DIFFRACTIONf_angle_d0.6214263
X-RAY DIFFRACTIONf_chiral_restr0.038485
X-RAY DIFFRACTIONf_plane_restr0.002550
X-RAY DIFFRACTIONf_dihedral_angle_d15.6771165
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.301-2.4780.327970.2981800189757
2.478-2.7280.3631370.2842369250675
2.728-3.1220.341440.2492840298489
3.122-3.9340.2391500.2033121327196
3.934-45.5320.2161780.1823221339997

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