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- PDB-7oxv: Crystal structure of depupylase Dop in the Dop-loop-inserted state -

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Basic information

Entry
Database: PDB / ID: 7oxv
TitleCrystal structure of depupylase Dop in the Dop-loop-inserted state
ComponentsDepupylase
KeywordsHYDROLASE / depupylase / Dop-loop / deamidase / Pup
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) / proteasomal protein catabolic process / modification-dependent protein catabolic process / peptidase activity / ATP binding / metal ion binding
Similarity search - Function
Pup deamidase / Pup ligase/deamidase / Pup-ligase protein
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / THIOCYANATE ION / Depupylase
Similarity search - Component
Biological speciesAcidothermus cellulolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.394 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2219
Polymers57,2881
Non-polymers9338
Water8,179454
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint23 kcal/mol
Surface area20210 Å2
Unit cell
Length a, b, c (Å)72.533, 72.533, 184.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1148-

HOH

21A-1150-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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)

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Non-polymers , 5 types, 462 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14-20 % (w/v) PEG 3350, 100 mM Bis-Tris propane pH 6.0-6.5 and 100-200 mM potassium thiocyanate (KSCN)
PH range: 6.0-6.5

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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: May 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→46.04 Å / Num. obs: 98553 / % possible obs: 99.85 % / Redundancy: 25.2 % / CC1/2: 1 / Net I/σ(I): 26.76
Reflection shellResolution: 1.39→1.444 Å / Redundancy: 22.6 % / Num. unique obs: 9612 / CC1/2: 0.587 / % possible all: 98.99

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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: 1.394→46.037 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 4965 5.04 %
Rwork0.1335 93574 -
obs0.1353 98539 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.82 Å2 / Biso mean: 28.2503 Å2 / Biso min: 6.41 Å2
Refinement stepCycle: final / Resolution: 1.394→46.037 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3980 0 68 454 4502
Biso mean--68.92 39.71 -
Num. residues----501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3941-1.40990.34081600.3086294297
1.4099-1.42650.33661520.25483112100
1.4265-1.44390.28031630.21593070100
1.4439-1.46220.21621720.18243066100
1.4622-1.48140.24621420.1673102100
1.4814-1.50170.2251620.14533065100
1.5017-1.52320.17781800.13133067100
1.5232-1.54590.20711470.13113098100
1.5459-1.57010.20581450.12873099100
1.5701-1.59580.18491680.1253091100
1.5958-1.62330.17991830.1183068100
1.6233-1.65280.16131680.11063098100
1.6528-1.68460.17791630.10863084100
1.6846-1.7190.14821570.1073086100
1.719-1.75640.1611690.10393076100
1.7564-1.79730.1521770.10433100100
1.7973-1.84220.16991600.10283090100
1.8422-1.8920.14331630.09923120100
1.892-1.94770.1541770.10093107100
1.9477-2.01060.14491750.10833123100
2.0106-2.08240.14751530.11343122100
2.0824-2.16580.1441680.11053116100
2.1658-2.26440.14011470.11533159100
2.2644-2.38370.15081610.12173134100
2.3837-2.53310.17071640.12883153100
2.5331-2.72860.16271910.1393144100
2.7286-3.00320.1611680.14643200100
3.0032-3.43760.18371750.14923194100
3.4376-4.33050.16341590.12783267100
4.3305-46.0370.18121960.16153421100

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