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- PDB-6gru: Crystal structure of human NUDT5 -

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Basic information

Entry
Database: PDB / ID: 6gru
TitleCrystal structure of human NUDT5
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / Nudix domain / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 8-oxo-GDP phosphatase activity / 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
ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsDubianok, Y. / Collins, P. / Krojer, T. / Fairhead, M. / MacLean, E. / Diaz Saez, L. / Strain-Damerell, C. / Elkins, J. / Burgess-Brown, N. / Bountra, C. ...Dubianok, Y. / Collins, P. / Krojer, T. / Fairhead, M. / MacLean, E. / Diaz Saez, L. / Strain-Damerell, C. / Elkins, J. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Huber, K. / von Delft, F. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of human NUDT5
Authors: Dubianok, Y. / Elkins, J. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Huber, K. / von Delft, F. / Structural Genomics Consortium (SGC)
History
DepositionJun 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,89815
Polymers92,5444
Non-polymers35411
Water4,053225
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4678
Polymers46,2722
Non-polymers1956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-97 kcal/mol
Surface area15950 Å2
MethodPISA
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4317
Polymers46,2722
Non-polymers1595
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6620 Å2
ΔGint-87 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.600, 60.140, 80.010
Angle α, β, γ (deg.)79.92, 81.52, 75.49
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALAAA14 - 20715 - 208
21LYSLYSALAALABB14 - 20715 - 208
12GLNGLNALAALAAA15 - 20716 - 208
22GLNGLNALAALACC15 - 20716 - 208
13LYSLYSALAALAAA14 - 20715 - 208
23LYSLYSALAALADD14 - 20715 - 208
14GLNGLNHISHISBB15 - 20616 - 207
24GLNGLNHISHISCC15 - 20616 - 207
15LYSLYSASNASNBB14 - 20815 - 209
25LYSLYSASNASNDD14 - 20815 - 209
16GLNGLNALAALACC15 - 20716 - 208
26GLNGLNALAALADD15 - 20716 - 208

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
ADP-sugar pyrophosphatase / 8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked ...8-oxo-dGDP phosphatase / Nuclear ATP-synthesis protein NUDIX5 / Nucleoside diphosphate-linked moiety X motif 5 / hNUDT5 / YSA1H


Mass: 23136.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5, NUDIX5, HSPC115 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UKK9, ADP-ribose diphosphatase, 8-oxo-dGDP phosphatase, ADP-D-ribose pyrophosphorylase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG4000, 0.2M magnesium chloride, 0.1M tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.93→43.49 Å / Num. obs: 64137 / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 7.4
Reflection shellResolution: 1.93→1.98 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DSD

2dsd


Resolution: 1.93→32.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.624 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 3176 4.9 %RANDOM
Rwork0.23115 ---
obs0.23298 60999 97.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.909 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å21.63 Å2-0.41 Å2
2---0.61 Å21.47 Å2
3----1.29 Å2
Refinement stepCycle: 1 / Resolution: 1.93→32.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5700 0 17 225 5942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0195826
X-RAY DIFFRACTIONr_bond_other_d0.0020.025327
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.987958
X-RAY DIFFRACTIONr_angle_other_deg0.964312318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7025763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96124.626227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.5915887
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9351530
X-RAY DIFFRACTIONr_chiral_restr0.10.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216543
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021079
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_it4.2164.4993073
X-RAY DIFFRACTIONr_mcbond_other4.2154.4993072
X-RAY DIFFRACTIONr_mcangle_it5.7826.7313829
X-RAY DIFFRACTIONr_mcangle_other5.7826.7313830
X-RAY DIFFRACTIONr_scbond_it4.364.7222753
X-RAY DIFFRACTIONr_scbond_other4.3594.7222753
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1966.974130
X-RAY DIFFRACTIONr_long_range_B_refined8.25352.055978
X-RAY DIFFRACTIONr_long_range_B_other8.25352.0535979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110520.05
12B110520.05
21A105860.08
22C105860.08
31A101300.09
32D101300.09
41B105180.09
42C105180.09
51B102500.09
52D102500.09
61C98400.1
62D98400.1
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 250 -
Rwork0.383 4417 -
obs--96.35 %

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