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Basic information

Entry
Database: PDB / ID: 5qja
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1497321453
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / NUDT5
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-K0A / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.64 Å
AuthorsDubianok, Y. / Collins, P. / Krojer, T. / Wright, N. / Strain-Damerell, C. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Huber, K. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Authors: Dubianok, Y. / Collins, P. / Krojer, T. / Wright, N. / Strain-Damerell, C. / Burgess-Brown, N. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / Huber, K. / von Delft, F.
History
DepositionOct 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2018Provider: 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)93,92622
Polymers92,5444
Non-polymers1,38118
Water4,954275
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,95011
Polymers46,2722
Non-polymers6779
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7690 Å2
ΔGint-93 kcal/mol
Surface area15620 Å2
MethodPISA
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,97611
Polymers46,2722
Non-polymers7049
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-77 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.437, 59.840, 80.189
Angle α, β, γ (deg.)79.330, 81.510, 75.500
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, 293 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-K0A / (2,5-dimethyl-1,3-thiazol-4-yl)(pyrrolidin-1-yl)methanone


Mass: 210.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H14N2OS
#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.: 275 / 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: 49.28 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris / PH range: pH

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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: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.64→78.36 Å / Num. obs: 102140 / % possible obs: 95.9 % / Redundancy: 1.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.026 / Rpim(I) all: 0.026 / Rrim(I) all: 0.036 / Net I/σ(I): 12.2 / Num. measured all: 176125 / 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
1.64-1.681.50.4071133373450.7860.4070.5761.193.8
7.33-78.361.80.012215011680.9990.0120.01747.698.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6GRU

6gru


Resolution: 1.64→78.35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.915 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 5140 5 %RANDOM
Rwork0.2254 ---
obs0.227 96986 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.95 Å2 / Biso mean: 32.371 Å2 / Biso min: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å21.06 Å20.08 Å2
2---0.58 Å20.89 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.64→78.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5748 0 85 275 6108
Biso mean--38.62 34.16 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027635
X-RAY DIFFRACTIONr_bond_other_d0.0020.026218
X-RAY DIFFRACTIONr_angle_refined_deg1.8611.9789423
X-RAY DIFFRACTIONr_angle_other_deg1.014314346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745907
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20824.098266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.851151004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4371539
X-RAY DIFFRACTIONr_chiral_restr0.1090.21056
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218158
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021349
X-RAY DIFFRACTIONr_mcbond_it2.6773.3053966
X-RAY DIFFRACTIONr_mcbond_other2.6773.3053967
X-RAY DIFFRACTIONr_mcangle_it3.774.9054479
LS refinement shellResolution: 1.639→1.682 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 367 -
Rwork0.367 6885 -
all-7252 -
obs--92.48 %

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