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- PDB-3aca: Crystal structure of human NUDT5 complexed with 8-oxo-dADP and ma... -

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Basic information

Entry
Database: PDB / ID: 3aca
TitleCrystal structure of human NUDT5 complexed with 8-oxo-dADP and manganese
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
Chem-8DD / : / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 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 30, 2009Deposition site: PDBJ / 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)44,5309
Polymers43,4012
Non-polymers1,1297
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-44 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.636, 40.701, 99.791
Angle α, β, γ (deg.)90.00, 121.64, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-437-

HOH

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Components

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


Mass: 21700.643 Da / Num. of mol.: 2 / Fragment: residues 13-208
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-8DD / 8-oxo-7,8-dihydro-2'-deoxy-adenosine-5'-diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.26 Å3/Da / Density % sol: 45.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1M Sodium Citrate, 30% PEG3350, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2009
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 24799 / Num. obs: 24799 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 28.67 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 37.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 5.3 / Num. unique all: 1212 / % possible all: 97.3

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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 3L85

3l85


Resolution: 2.05→34.893 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.813 / SU ML: 0.14 / σ(F): 1.35 / Phase error: 25.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1194 4.82 %RANDOM
Rwork0.199 ---
obs0.201 24791 99.28 %-
all-24799 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.096 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 104.33 Å2 / Biso mean: 36.447 Å2 / Biso min: 10.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.229 Å20 Å2-0.27 Å2
2--0.85 Å2-0 Å2
3----0.621 Å2
Refinement stepCycle: LAST / Resolution: 2.05→34.893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3038 0 59 250 3347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023154
X-RAY DIFFRACTIONf_angle_d0.5844297
X-RAY DIFFRACTIONf_chiral_restr0.037488
X-RAY DIFFRACTIONf_plane_restr0.002551
X-RAY DIFFRACTIONf_dihedral_angle_d16.3661179
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.1260.3151120.2452505261796
2.126-2.2230.2741470.2232577272499
2.223-2.340.2951250.212591271699
2.34-2.4860.2771450.21526142759100
2.486-2.6780.2951270.22526312758100
2.678-2.9480.2951310.22526262757100
2.948-3.3740.2751310.20426632794100
3.374-4.250.211500.17126362786100
4.25-34.8980.1871260.17127542880100

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