[English] 日本語
Yorodumi
- PDB-7oy3: Crystal structure of depupylase Dop in complex with phosphorylate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7oy3
TitleCrystal structure of depupylase Dop in complex with phosphorylated Pup and ADP
Components
  • Depupylase
  • Prokaryotic ubiquitin-like protein Pup
KeywordsHYDROLASE / depupylase / ATP hydrolysis / deamidase / phosphorylated 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 / : / 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: 1.78 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 2.0Mar 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_poly_seq_scheme / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif
Item: _atom_site.auth_atom_id / _atom_site.auth_comp_id ..._atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,95418
Polymers60,5682
Non-polymers1,38616
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-18 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.806, 106.806, 108.457
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
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: 3279.369 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The C-terminal glumate (E) of this peptide was phosphorylated in the presence of ATP during crystallization. The phosphorylated glumate was renamed as GLP.
Source: (synth.) Acidothermus cellulolyticus (bacteria) / References: UniProt: A0LU49

-
Non-polymers , 8 types, 479 molecules

#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: 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
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.28 %
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 and 0.75-1.0 M KH2PO4
PH range: 7.0-8.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.815 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.775577→47.9101 Å / Num. obs: 68753 / % possible obs: 99.83 % / Redundancy: 20.6 % / CC1/2: 0.999 / Net I/σ(I): 12.56
Reflection shellResolution: 1.78→1.844 Å / Num. unique obs: 6798 / CC1/2: 0.774

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LRT

5lrt


Resolution: 1.78→46.78 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 6365 4.77 %
Rwork0.1699 127000 -
obs0.1711 68738 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.32 Å2 / Biso mean: 30.5869 Å2 / Biso min: 14.86 Å2
Refinement stepCycle: final / Resolution: 1.78→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 87 463 4523
Biso mean--46.72 38.74 -
Num. residues----499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.80.35631920.3314014420695
1.8-1.820.29471690.289443354504100
1.82-1.840.2692140.270842014415100
1.84-1.860.2742040.266442764480100
1.86-1.890.29021840.24142464430100
1.89-1.910.26582380.239442324470100
1.91-1.940.23792600.234541964456100
1.94-1.970.24042400.22942254465100
1.97-20.23442320.212942094441100
2-2.030.22811820.199142714453100
2.03-2.070.2332360.194241634399100
2.07-2.110.24311860.195543254511100
2.11-2.150.22822500.189542274477100
2.15-2.190.23122160.185141744390100
2.19-2.240.19671760.177743334509100
2.24-2.290.19071640.182542164380100
2.29-2.350.22372020.172943254527100
2.35-2.410.19212000.176442384438100
2.41-2.480.19942260.168942074433100
2.48-2.560.17942380.1741764414100
2.56-2.650.22172140.164442414455100
2.65-2.760.1872080.165142834491100
2.76-2.880.21712450.170142284473100
2.88-3.030.18082140.166341974411100
3.04-3.230.21421820.167942964478100
3.23-3.470.17042040.160942764480100
3.48-3.820.17892300.139242044434100
3.83-4.380.16322150.125542374452100
4.38-5.510.13912300.13942094439100
5.52-46.780.15552140.157642404454100

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more