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- PDB-5r5k: PanDDA analysis group deposition -- Crystal Structure of human NU... -

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Basic information

Entry
Database: PDB / ID: 5r5k
TitlePanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13960a
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 / Chem-S2J / Uridine diphosphate glucose pyrophosphatase NUDT22
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.6 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)33,2636
Polymers32,7071
Non-polymers5565
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.480, 52.310, 101.620
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-S2J / methyl 2-[(2~{R})-1-(ethylcarbamoyl)-3-oxidanylidene-piperazin-2-yl]ethanoate


Mass: 243.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O4
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


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


Mass: 18.015 Da / Num. of mol.: 161 / 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: 38.82 % / 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: 1.6→27.95 Å / Num. obs: 35575 / % possible obs: 99.9 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Net I/σ(I): 9.4 / Num. measured all: 226381 / 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
1.6-1.646.51.6861700025970.6050.7051.831.199.9
7.16-27.955.80.03826904640.9990.0170.04232.798.4

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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: 1.6→27.97 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.101 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1928 5.4 %RANDOM
Rwork0.1897 ---
obs0.192 33593 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 157.31 Å2 / Biso mean: 25.667 Å2 / Biso min: 16.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.41 Å2-0 Å20 Å2
2---2.36 Å2-0 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 1.6→27.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 33 161 2392
Biso mean--53.51 39.13 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172312
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.643532
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5725352
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.01321.448145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.57115374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3821516
X-RAY DIFFRACTIONr_chiral_restr0.080.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023059
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02537
X-RAY DIFFRACTIONr_mcbond_it1.9312.5031367
X-RAY DIFFRACTIONr_mcbond_other1.9182.4991365
X-RAY DIFFRACTIONr_mcangle_it2.6873.7341656
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 154 -
Rwork0.352 2430 -
all-2584 -
obs--99.69 %

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