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- PDB-5r56: PanDDA analysis group deposition -- Crystal Structure of human NU... -

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Basic information

Entry
Database: PDB / ID: 5r56
TitlePanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13688a
ComponentsUridine diphosphate glucose pyrophosphatase NUDT22
KeywordsHYDROLASE / PanDDA / SGC - Diamond I04-1 fragment screening / NUDIX domain / XChemExplorer / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 22
Function / homologyGDP-mannose hydrolase activity / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / Nudix hydrolase domain profile. / NUDIX hydrolase domain / nucleoplasm / metal ion binding / 2-(2,4-dimethylphenoxy)-1-morpholin-4-yl-ethanone / Uridine diphosphate glucose pyrophosphatase NUDT22
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.51 Å
AuthorsDiaz-Saez, L. / Talon, R. / Krojer, T. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Huber, K.V.M.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Diaz-Saez, L. / Talon, R. / Krojer, T. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Huber, K.V.M.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine diphosphate glucose pyrophosphatase NUDT22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4258
Polymers32,7071
Non-polymers7187
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.590, 52.330, 101.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uridine diphosphate glucose pyrophosphatase NUDT22 / UGPPase / Nucleoside diphosphate-linked moiety X motif 22 / Nudix motif 22


Mass: 32706.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT22, PP11246 / Production host: escherichia coli (E. coli) / References: UniProt: Q9BRQ3, UDP-sugar diphosphatase
#2: Chemical ChemComp-S07 / 2-(2,4-dimethylphenoxy)-1-morpholin-4-yl-ethanone


Mass: 249.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19NO3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.01 Å3/Da / Density % sol: 38.94 % / Mosaicity: 0 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.51→50.78 Å / Num. obs: 42305 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.031 / Rrim(I) all: 0.08 / Net I/σ(I): 12.7 / Num. measured all: 273386 / 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
1.51-1.556.51.5821988930720.5210.6741.7221.299.8
6.75-50.785.70.02832165650.9990.0120.0346.599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.5.26data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LF9

5lf9


Resolution: 1.51→50.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.253 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2156 2269 5.4 %RANDOM
Rwork0.1839 ---
obs0.1857 39971 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 228.41 Å2 / Biso mean: 24.013 Å2 / Biso min: 14.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å2-0 Å20 Å2
2---1.72 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: final / Resolution: 1.51→50.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 42 163 2403
Biso mean--54.94 38.06 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0143399
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172661
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6414126
X-RAY DIFFRACTIONr_angle_other_deg1.3741.5726172
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6395403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.67321.84163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64715428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7531519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023619
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02650
X-RAY DIFFRACTIONr_mcbond_it1.6372.3141689
X-RAY DIFFRACTIONr_mcbond_other1.6262.3021675
X-RAY DIFFRACTIONr_mcangle_it2.4923.4231935
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 160 -
Rwork0.323 2900 -
all-3060 -
obs--99.71 %

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