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- PDB-5r55: PanDDA analysis group deposition -- Crystal Structure of human NU... -

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Basic information

Entry
Database: PDB / ID: 5r55
TitlePanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13369a
ComponentsUridine diphosphate glucose pyrophosphatase NUDT22
KeywordsHYDROLASE / PanDDA / SGC - Diamond I04-1 fragment screening / NUDIX domain / XChemExplorer / NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 22
Function / homology
Function and homology information


GDP-mannose hydrolase activity / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / nucleoplasm / metal ion binding
Similarity search - Function
: / Nudix hydrolase domain profile. / NUDIX hydrolase domain
Similarity search - Domain/homology
~{N}-methyl-1-pyridin-4-yl-methanamine / Uridine diphosphate glucose pyrophosphatase NUDT22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.48 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)33,0635
Polymers32,7071
Non-polymers3574
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.720, 52.370, 101.890
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-RYP / ~{N}-methyl-1-pyridin-4-yl-methanamine


Mass: 122.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10N2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.03 Å3/Da / Density % sol: 39.35 % / 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: 1.48→46.58 Å / Num. obs: 45159 / % possible obs: 99.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.071 / Net I/σ(I): 15.3 / Num. measured all: 293281 / 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
1.48-1.526.11.5812010232700.4920.691.7291.299.7
6.62-46.585.80.02934345910.9990.0130.03259.899.2

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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: 1.48→46.62 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.829 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 2431 5.4 %RANDOM
Rwork0.1896 ---
obs0.1912 42662 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 434.37 Å2 / Biso mean: 22.118 Å2 / Biso min: 13.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.66 Å20 Å2-0 Å2
2---1.58 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.48→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 21 159 2378
Biso mean--43.59 39.47 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172279
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.6443481
X-RAY DIFFRACTIONr_angle_other_deg1.4321.5845289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91622.734128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.31215374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1341516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023005
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02517
X-RAY DIFFRACTIONr_mcbond_it1.9792.131374
X-RAY DIFFRACTIONr_mcbond_other1.9562.1211365
X-RAY DIFFRACTIONr_mcangle_it2.793.1651656
LS refinement shellResolution: 1.48→1.518 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 189 -
Rwork0.329 3074 -
all-3263 -
obs--99.57 %

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