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

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Basic information

Entry
Database: PDB / ID: 5qgv
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with UNUYB062989
ComponentsPeroxisomal coenzyme A diphosphatase NUDT7
KeywordsHYDROLASE / PanDDA / SGC - Diamond I04-1 fragment screening / NUDIX domain / XChemExplorer
Function / homology
Function and homology information


butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / medium-chain fatty-acyl-CoA catabolic process / coenzyme A diphosphatase / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process ...butyryl-CoA catabolic process / propionyl-CoA metabolic process / propionyl-CoA catabolic process / medium-chain fatty-acyl-CoA catabolic process / coenzyme A diphosphatase / malonyl-CoA catabolic process / Peroxisomal lipid metabolism / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process / nucleoside diphosphate metabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / peroxisomal matrix / brown fat cell differentiation / Peroxisomal protein import / peroxisome / manganese ion binding / magnesium ion binding / cytosol
Similarity search - Function
NUDIX hydrolase, NudL, conserved site / Nudix CoA signature. / Coenzyme A pyrophosphatase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / N-(3-chlorophenyl)-2-(3-methoxyphenyl)acetamide / Peroxisomal coenzyme A diphosphatase NUDT7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.59 Å
AuthorsKrojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. ...Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, J. / Spencer, J. / London, N. / Nelson, A. / Brennan, P.E. / Huber, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: To Be Published
Title: PanDDA analysis group deposition of models with modelled events (e.g. bound ligands)
Authors: Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, ...Authors: Krojer, T. / Talon, R. / Fairhead, M. / Diaz Saez, L. / Bradley, A.R. / Aimon, A. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Ruda, G.F. / Szommer, T. / Srikannathasan, V. / Elkins, J. / Spencer, J. / London, N. / Nelson, A. / Brennan, P.E. / Huber, K. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
History
DepositionMay 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: 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: Peroxisomal coenzyme A diphosphatase NUDT7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7486
Polymers22,1981
Non-polymers5505
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint4 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.333, 124.333, 41.009
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Peroxisomal coenzyme A diphosphatase NUDT7 / Nucleoside diphosphate-linked moiety X motif 7 / Nudix motif 7


Mass: 22197.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT7 / Production host: Escherichia coli (E. coli)
References: UniProt: P0C024, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-H3A / N-(3-chlorophenyl)-2-(3-methoxyphenyl)acetamide


Mass: 275.730 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14ClNO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 4.12 Å3/Da / Density % sol: 70.16 % / Mosaicity: 0.08 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M bis-tris pH 5.5 -- 0.1M ammonium acetate -- 5%(w/v) PEG10K

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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: May 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.59→29.86 Å / Num. obs: 48790 / % possible obs: 99.9 % / Redundancy: 11.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.016 / Rrim(I) all: 0.052 / Net I/σ(I): 24.9 / Num. measured all: 547122 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1 / % possible all: 98.7

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.59-1.63110.8243928435730.8640.2580.8652.7
7.12-29.8611.20.03966105900.9970.0130.04168.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0189refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5T3P

5t3p


Resolution: 1.59→107.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.393 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.065 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 2589 5.3 %RANDOM
Rwork0.1948 ---
obs0.1956 46200 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.03 Å2 / Biso mean: 31.948 Å2 / Biso min: 15.31 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å2-0 Å2
3----0.9 Å2
Refinement stepCycle: final / Resolution: 1.59→107.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1467 0 35 160 1662
Biso mean--46.87 42.61 -
Num. residues----186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191561
X-RAY DIFFRACTIONr_bond_other_d0.0020.021469
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9882122
X-RAY DIFFRACTIONr_angle_other_deg0.9322.9883408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28624.26568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26915255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.681158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211723
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02301
X-RAY DIFFRACTIONr_mcbond_it2.092.851759
X-RAY DIFFRACTIONr_mcbond_other2.0692.84756
X-RAY DIFFRACTIONr_mcangle_it3.2354.242948
LS refinement shellResolution: 1.593→1.634 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 177 -
Rwork0.267 3397 -
all-3574 -
obs--98.95 %

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