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- PDB-5qk7: PanDDA analysis group deposition of models with modelled events (... -

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Basic information

Entry
Database: PDB / ID: 5qk7
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z1918536193
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-K3P / ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.66 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)93,86521
Polymers92,5444
Non-polymers1,32117
Water4,486249
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,95011
Polymers46,2722
Non-polymers6789
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7550 Å2
ΔGint-89 kcal/mol
Surface area15680 Å2
MethodPISA
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,91510
Polymers46,2722
Non-polymers6438
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-81 kcal/mol
Surface area15680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.577, 59.461, 80.404
Angle α, β, γ (deg.)79.390, 82.310, 76.190
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, 266 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-K3P / 5-chloro-4-[(1-methyl-1H-pyrazol-4-yl)oxy]pyrimidine


Mass: 210.620 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7ClN4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.38 Å3/Da / Density % sol: 48.42 % / Mosaicity: 0.29 °
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 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.66→46.96 Å / Num. obs: 88015 / % possible obs: 87.7 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.036 / Rrim(I) all: 0.051 / Net I/σ(I): 7.5 / Num. measured all: 155480 / 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
1.66-1.751.71.24523708139240.3891.2451.7610.594.8
5.26-46.961.80.025517229290.9970.0250.03522.392.1

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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: 1.66→78.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.642 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2549 4470 5.1 %RANDOM
Rwork0.2167 ---
obs0.2186 83543 87.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.76 Å2 / Biso mean: 39.196 Å2 / Biso min: 21.03 Å2
Baniso -1Baniso -2Baniso -3
1-4 Å21.26 Å20.6 Å2
2---1.46 Å21.08 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 1.66→78.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 81 249 6084
Biso mean--51.48 41.94 -
Num. residues----770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.027396
X-RAY DIFFRACTIONr_bond_other_d0.0020.025952
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9829157
X-RAY DIFFRACTIONr_angle_other_deg1.006313766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.115889
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1124.525263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4115984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8181534
X-RAY DIFFRACTIONr_chiral_restr0.1040.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218209
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021313
X-RAY DIFFRACTIONr_mcbond_it3.133.953861
X-RAY DIFFRACTIONr_mcbond_other3.133.953862
X-RAY DIFFRACTIONr_mcangle_it4.5745.894363
LS refinement shellResolution: 1.664→1.707 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 399 -
Rwork0.412 6630 -
all-7029 -
obs--94.48 %

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