[English] 日本語
Yorodumi
- PDB-8hm3: Complex of PPIase-BfUbb -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hm3
TitleComplex of PPIase-BfUbb
Components
  • Peptidylprolyl isomerase
  • Putative ubiquitin
KeywordsISOMERASE / human ubiquitin-like protein
Function / homology
Function and homology information


peptidyl-prolyl cis-trans isomerase activity
Similarity search - Function
Trigger factor/SurA domain superfamily / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin / PpiC domain-containing protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsXu, J.H. / Chen, Z. / Gao, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32122007 China
CitationJournal: Nat Microbiol / Year: 2024
Title: Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome.
Authors: Jiang, K. / Li, W. / Tong, M. / Xu, J. / Chen, Z. / Yang, Y. / Zang, Y. / Jiao, X. / Liu, C. / Lim, B. / Jiang, X. / Wang, J. / Wu, D. / Wang, M. / Liu, S.J. / Shao, F. / Gao, X.
History
DepositionDec 2, 2022Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative ubiquitin
B: Peptidylprolyl isomerase
C: Putative ubiquitin
D: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,93511
Polymers116,3544
Non-polymers5817
Water11,097616
1
A: Putative ubiquitin
B: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6427
Polymers58,1772
Non-polymers4645
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-30 kcal/mol
Surface area27680 Å2
MethodPISA
2
C: Putative ubiquitin
D: Peptidylprolyl isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2944
Polymers58,1772
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-15 kcal/mol
Surface area27750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.860, 100.920, 106.180
Angle α, β, γ (deg.)90.000, 100.463, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Putative ubiquitin


Mass: 8791.050 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: ubb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5L8M7
#2: Protein Peptidylprolyl isomerase


Mass: 49386.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: BN669_00367 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: R6ZJY1

-
Non-polymers , 4 types, 623 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 14% PEG3350, 0.3M magnesium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.26→30.74 Å / Num. obs: 59756 / % possible obs: 99.37 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.43 Å2 / CC1/2: 0.993 / Net I/σ(I): 12.7
Reflection shellResolution: 2.26→2.34 Å / Num. unique obs: 5944 / CC1/2: 0.606 / % possible all: 99.68

-
Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.19.2_4158refinement
MOLREPphasing
DMphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 2.26→30.74 Å / SU ML: 0.3728 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.6155
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2604 2969 4.97 %
Rwork0.2135 56780 -
obs0.2158 59749 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.54 Å2
Refinement stepCycle: LAST / Resolution: 2.26→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8145 0 36 616 8797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00758308
X-RAY DIFFRACTIONf_angle_d1.029611187
X-RAY DIFFRACTIONf_chiral_restr0.06021226
X-RAY DIFFRACTIONf_plane_restr0.00661461
X-RAY DIFFRACTIONf_dihedral_angle_d16.04543242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.30.35061450.28972693X-RAY DIFFRACTION99.68
2.3-2.340.36391480.28212653X-RAY DIFFRACTION99.64
2.34-2.380.39151450.27862737X-RAY DIFFRACTION99.76
2.38-2.420.3181350.28252693X-RAY DIFFRACTION99.75
2.42-2.470.30481520.26762708X-RAY DIFFRACTION99.65
2.47-2.530.3091380.25882704X-RAY DIFFRACTION99.65
2.53-2.590.31991340.26182704X-RAY DIFFRACTION99.82
2.59-2.650.34581410.26262691X-RAY DIFFRACTION99.75
2.65-2.720.32311430.26252702X-RAY DIFFRACTION99.51
2.72-2.80.32571380.25432728X-RAY DIFFRACTION99.58
2.8-2.890.32221430.23992682X-RAY DIFFRACTION99.75
2.89-30.29541380.23562682X-RAY DIFFRACTION99.54
3-3.120.2951370.2292731X-RAY DIFFRACTION99.31
3.12-3.260.30841370.24562727X-RAY DIFFRACTION99.55
3.26-3.430.29961150.22542708X-RAY DIFFRACTION99.19
3.43-3.650.26741430.20872718X-RAY DIFFRACTION99.58
3.65-3.930.27111550.19912679X-RAY DIFFRACTION99.09
3.93-4.320.20881310.17462708X-RAY DIFFRACTION98.92
4.32-4.950.21500.16682674X-RAY DIFFRACTION98.47
4.95-6.230.21511590.19072711X-RAY DIFFRACTION98.46
6.23-30.740.16031420.16552747X-RAY DIFFRACTION98.53

+
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://pdbjlvh1.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