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

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Basic information

Entry
Database: PDB / ID: 5qha
TitlePanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT7 in complex with PCM-0102951
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 / Peroxisomal lipid metabolism / malonyl-CoA catabolic process / 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 / Peroxisomal lipid metabolism / malonyl-CoA catabolic process / coenzyme A diphosphatase activity / coenzyme A catabolic process / acetyl-CoA catabolic process / succinyl-CoA catabolic process / nucleoside diphosphate metabolic process / snoRNA binding / peroxisomal matrix / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / 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 / Chem-H3D / Peroxisomal coenzyme A diphosphatase NUDT7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.57 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
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
DepositionSep 21, 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)22,5774
Polymers22,1981
Non-polymers3793
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-0 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.800, 123.800, 41.060
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-H3D / N-[1-(2,3-dihydro-1,4-benzodioxin-6-yl)cyclopentyl]acetamide


Mass: 261.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H19NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 4.09 Å3/Da / Density % sol: 69.94 % / Mosaicity: 0 °
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: Sep 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.57→53.61 Å / Num. obs: 50185 / % possible obs: 99.3 % / Redundancy: 7.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.043 / Rrim(I) all: 0.129 / Net I/σ(I): 8.2 / Num. measured all: 388598 / Scaling rejects: 15
Reflection shellResolution: 1.57→1.61 Å / Redundancy: 5.8 % / Rmerge(I) obs: 2.865 / Num. measured all: 20976 / Num. unique all: 3598 / CC1/2: 0.534 / Rpim(I) all: 1.28 / Rrim(I) all: 3.147 / Net I/σ(I) obs: 0.5 / % possible all: 97.5

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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: 1.57→107.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 6.081 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2425 4.9 %RANDOM
Rwork0.194 ---
obs0.196 47257 98.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.66 Å2 / Biso mean: 30.8 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å2-0.82 Å20 Å2
2---1.63 Å20 Å2
3---5.3 Å2
Refinement stepCycle: final / Resolution: 1.57→107.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1449 0 27 175 1651
Biso mean--49.06 46.99 -
Num. residues----185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191539
X-RAY DIFFRACTIONr_bond_other_d0.0020.021430
X-RAY DIFFRACTIONr_angle_refined_deg1.8132.0032100
X-RAY DIFFRACTIONr_angle_other_deg1.05733326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2975189
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91824.47867
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.049157
X-RAY DIFFRACTIONr_chiral_restr0.1130.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211702
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7272.729755
X-RAY DIFFRACTIONr_mcbond_other4.7242.729756
X-RAY DIFFRACTIONr_mcangle_it5.7534.087944
X-RAY DIFFRACTIONMAIN-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONSIDE-CHAIN BOND OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONSIDE-CHAIN ANGLE OTHER ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B REFINED ATOMS (A**2)
X-RAY DIFFRACTIONLONG RANGE B OTHER ATOMS (A**2)
X-RAY DIFFRACTIONr_rigid_bond_restr2.77932967
X-RAY DIFFRACTIONr_sphericity_free45.604597
X-RAY DIFFRACTIONr_sphericity_bonded22.81753008
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.514 153 -
Rwork0.491 3339 -
all-3492 -
obs--94.63 %

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