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- PDB-5qto: PanDDA analysis group deposition -- Crystal Structure of NUDT5 in... -

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Basic information

Entry
Database: PDB / ID: 5qto
TitlePanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with 1R-0641
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / 8-oxo-GDP phosphatase activity / ADP-ribose diphosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / 8-oxo-GDP phosphatase activity / ADP-ribose diphosphatase activity / D-ribose catabolic process / 8-oxo-dGDP phosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-PWG / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.67 Å
AuthorsDubianok, Y. / Krojer, T. / Kovacs, H. / Moriaud, F. / Wright, N. / Strain-Damerell, C. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Dubianok, Y. / Krojer, T. / Kovacs, H. / Moriaud, F. / Wright, N. / Strain-Damerell, C. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
History
DepositionAug 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_contact_author / pdbx_entry_details / Item: _pdbx_contact_author.country

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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)94,03322
Polymers92,5444
Non-polymers1,48918
Water4,612256
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,06512
Polymers46,2722
Non-polymers79310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-89 kcal/mol
Surface area15570 Å2
MethodPISA
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,96810
Polymers46,2722
Non-polymers6968
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-83 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.260, 59.871, 79.887
Angle α, β, γ (deg.)79.470, 81.460, 75.590
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#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

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Non-polymers , 5 types, 274 molecules

#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-PWG / 3-(difluoromethyl)-8-(trifluoromethyl)[1,2,4]triazolo[4,3-a]pyridine


Mass: 237.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H4F5N3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 256 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 2.41 Å3/Da / Density % sol: 48.96 % / Mosaicity: 0.15 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 33% PEG4000, 0.2 magnesium chloride, 0.1 M Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.67→41.48 Å / Num. obs: 95026 / % possible obs: 94.2 % / Redundancy: 1.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.033 / Rrim(I) all: 0.047 / Net I/σ(I): 9.5 / Num. measured all: 166019 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.67-1.761.50.88521069138640.4320.8851.2510.893.9
5.27-41.481.80.017544730200.9990.0170.02433.194.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 6GRU

6gru


Resolution: 1.67→41.52 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.302 / SU ML: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.144 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2618 4724 5 %RANDOM
Rwork0.2294 ---
obs0.231 89541 93.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 99.2 Å2 / Biso mean: 38.281 Å2 / Biso min: 16.93 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å21.15 Å20.16 Å2
2---0.65 Å20.58 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 1.67→41.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5784 0 93 256 6133
Biso mean--48.72 38.27 -
Num. residues----774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0148892
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176693
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.67810462
X-RAY DIFFRACTIONr_angle_other_deg1.2971.58315432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.54751016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37522.648321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.977151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1471537
X-RAY DIFFRACTIONr_chiral_restr0.0640.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029285
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021562
X-RAY DIFFRACTIONr_mcbond_it2.644.2924657
X-RAY DIFFRACTIONr_mcbond_other2.6544.2994600
X-RAY DIFFRACTIONr_mcangle_it4.1036.2274980
LS refinement shellResolution: 1.667→1.71 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 325 -
Rwork0.455 6076 -
all-6401 -
obs--86 %

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