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

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Basic information

Entry
Database: PDB / ID: 5qts
TitlePanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with 8J-537S
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 / D-ribose catabolic process / ADP-ribose diphosphatase activity / 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 / D-ribose catabolic process / ADP-ribose diphosphatase activity / 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-PWS / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.85 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)94,16825
Polymers92,5444
Non-polymers1,62321
Water4,774265
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,16414
Polymers46,2722
Non-polymers89112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-83 kcal/mol
Surface area15630 Å2
MethodPISA
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,00411
Polymers46,2722
Non-polymers7329
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-75 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.315, 59.910, 80.078
Angle α, β, γ (deg.)79.340, 81.270, 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, 286 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-PWS / 3-methyl-2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one


Mass: 224.203 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7F3N2OS
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.42 Å3/Da / Density % sol: 49.14 % / Mosaicity: 0 °
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: May 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.85→50.06 Å / Num. obs: 71454 / % possible obs: 96.4 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.056 / Net I/σ(I): 9.6 / Num. measured all: 125372 / 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
1.85-1.91.80.718956152830.6430.7181.0160.995.5
8.27-50.061.90.01515238130.9990.0150.02134.998.4

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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: 1.85→50.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.232 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3582 5 %RANDOM
Rwork0.2165 ---
obs0.2182 67844 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.93 Å2 / Biso mean: 35.868 Å2 / Biso min: 15.92 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20.96 Å20.31 Å2
2---0.77 Å20.88 Å2
3----1.41 Å2
Refinement stepCycle: final / Resolution: 1.85→50.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5818 0 97 265 6180
Biso mean--44.81 34.74 -
Num. residues----775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01410658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177795
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.6811855
X-RAY DIFFRACTIONr_angle_other_deg1.2751.59118068
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41351201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.39722.153367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3361553
X-RAY DIFFRACTIONr_chiral_restr0.0630.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210511
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021724
X-RAY DIFFRACTIONr_mcbond_it2.3293.9345672
X-RAY DIFFRACTIONr_mcbond_other2.3433.9435604
X-RAY DIFFRACTIONr_mcangle_it3.7635.7275797
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 281 -
Rwork0.364 4877 -
all-5158 -
obs--93.1 %

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