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- PDB-7oyf: Crystal structure of depupylase Dop in complex with Pup and ADP/t... -

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Basic information

Entry
Database: PDB / ID: 7oyf
TitleCrystal structure of depupylase Dop in complex with Pup and ADP/trifluoromagnesate
Components
  • Depupylase
  • Prokaryotic ubiquitin-like protein Pup
KeywordsHYDROLASE / depupylase / transition state / deamidase / Pup binding
Function / homology
Function and homology information


protein pupylation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on peptide bonds (peptidases) / proteasome binding / proteasomal protein catabolic process / modification-dependent protein catabolic process / protein tag activity / peptidase activity / ATP binding / metal ion binding
Similarity search - Function
Pup deamidase / Pup ligase/deamidase / Pup-ligase protein / Prokaryotic ubiquitin-like protein Pup / Pup-like protein
Similarity search - Domain/homology
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / trifluoromagnesate monohydrate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Depupylase / Prokaryotic ubiquitin-like protein Pup
Similarity search - Component
Biological speciesAcidothermus cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å
AuthorsCui, H.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_163314 Switzerland
CitationJournal: Nat Commun / Year: 2021
Title: Structures of prokaryotic ubiquitin-like protein Pup in complex with depupylase Dop reveal the mechanism of catalytic phosphate formation.
Authors: Cui, H. / Muller, A.U. / Leibundgut, M. / Tian, J. / Ban, N. / Weber-Ban, E.
History
DepositionJun 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Depupylase
B: Prokaryotic ubiquitin-like protein Pup
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,24120
Polymers60,4882
Non-polymers1,75418
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-24 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.334, 106.334, 107.384
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein Depupylase


Mass: 57288.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The C-terminal ENLYFQ fragment is a leftover from TEV clevage site.
Source: (gene. exp.) Acidothermus cellulolyticus (bacteria) / Gene: dop, Acel_1186 / Production host: Escherichia coli (E. coli)
References: UniProt: A0LU48, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein/peptide Prokaryotic ubiquitin-like protein Pup / Bacterial ubiquitin-like modifier


Mass: 3199.389 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This is a C-terminal half fragment of the full length Pup.
Source: (synth.) Acidothermus cellulolyticus (bacteria) / References: UniProt: A0LU49

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Non-polymers , 8 types, 319 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#9: Chemical ChemComp-KQB / trifluoromagnesate monohydrate


Mass: 97.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3MgO / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.9 Å3/Da / Density % sol: 57.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM Tris-acetate pH 7.0-8.5, 10 mM ADP, 40 mM MgCl2, 16 mM NaF, 4 mM BeSO4 and 0.75-1.0 M KH2PO4
PH range: 7.0-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.88→47.65 Å / Num. obs: 57471 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 29.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.03 / Rrim(I) all: 0.134 / Net I/σ(I): 15.5 / Num. measured all: 1162247 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.88-1.9219.81.727261236740.7850.3961.7652.1100
9.02-47.6517.80.043106425980.9990.010.04448.999.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRT

5lrt


Resolution: 1.88→47.65 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 2960 5.15 %
Rwork0.159 54469 -
obs0.1605 57429 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.97 Å2 / Biso mean: 33.8445 Å2 / Biso min: 18.3 Å2
Refinement stepCycle: final / Resolution: 1.88→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 111 301 4398
Biso mean--50.47 40.5 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.88-1.910.2881490.225325602709
1.91-1.940.24291220.213225802702
1.94-1.980.2511390.211425762715
1.98-2.020.2061260.193625732699
2.02-2.060.24171230.185225542677
2.06-2.10.1881260.168725942720
2.1-2.150.21561390.168225732712
2.15-2.210.1861330.162125702703
2.21-2.270.20831290.159326082737
2.27-2.330.20171120.15826042716
2.33-2.410.19311580.153525462704
2.41-2.490.22611470.160225762723
2.49-2.590.1771510.155225902741
2.59-2.710.1941480.157625592707
2.71-2.850.21621440.168725952739
2.85-3.030.20451660.169425792745
3.03-3.270.20541270.183126162743
3.27-3.60.16161570.156425882745
3.6-4.120.1711460.138726352781
4.12-5.180.15211720.132226252797
5.19-47.650.19061460.158827682914

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