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- PDB-7oxy: Crystal structure of depupylase Dop in complex with Pup and AMP-PCP -

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Basic information

Entry
Database: PDB / ID: 7oxy
TitleCrystal structure of depupylase Dop in complex with Pup and AMP-PCP
Components
  • Depupylase
  • Prokaryotic ubiquitin-like protein Pup
KeywordsHYDROLASE / depupylase / ATP hydrolysis / 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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ACETATE ION / 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: 1.65 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 23, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)62,25421
Polymers60,4872
Non-polymers1,76819
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-31 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.668, 106.668, 108.791
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: 3198.405 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This is only the C-terminal half of the Pup protein.
Source: (synth.) Acidothermus cellulolyticus (strain ATCC 43068 / 11B) (bacteria)
References: UniProt: A0LU49

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Non-polymers , 7 types, 345 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.95 Å3/Da / Density % sol: 58.36 %
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 AMP-PCP, 40 mM MgCl2 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: 1.65→46.19 Å / Num. obs: 86165 / % possible obs: 99.98 % / Redundancy: 20.2 % / CC1/2: 1 / Net I/σ(I): 21.3
Reflection shellResolution: 1.65→1.709 Å / Num. unique obs: 8506 / CC1/2: 0.746

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRT

5lrt


Resolution: 1.65→46.189 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 4381 5.09 %
Rwork0.1729 81771 -
obs0.1742 86152 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.13 Å2 / Biso mean: 33.4008 Å2 / Biso min: 18.01 Å2
Refinement stepCycle: final / Resolution: 1.65→46.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3986 0 119 326 4431
Biso mean--48.91 40.57 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.65-1.66880.3181390.2922655
1.6688-1.68840.2571190.26272767
1.6884-1.7090.25941520.23792673
1.709-1.73060.27051300.24052731
1.7306-1.75340.23241540.22282690
1.7534-1.77740.22471560.2132686
1.7774-1.80280.22121460.20652666
1.8028-1.82970.25361240.20782740
1.8297-1.85830.23191530.20172703
1.8583-1.88880.24221690.19782657
1.8888-1.92130.24511390.1962708
1.9213-1.95630.21071440.19872704
1.9563-1.99390.2081470.20582688
1.9939-2.03460.20831300.18042762
2.0346-2.07890.21341310.18472711
2.0789-2.12720.19241330.18132732
2.1272-2.18040.23211860.18072688
2.1804-2.23940.19981500.18412711
2.2394-2.30530.21471360.18472749
2.3053-2.37970.2171230.17952744
2.3797-2.46470.20961690.17382693
2.4647-2.56340.21151460.17872705
2.5634-2.680.21181330.17072768
2.68-2.82130.18541530.18082740
2.8213-2.9980.18761350.17882719
2.998-3.22950.18851330.18252779
3.2295-3.55440.18981400.16392773
3.5544-4.06840.18031480.14652761
4.0684-5.12470.17321830.13682783
5.1247-46.1890.17511800.16982885

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