[English] 日本語
Yorodumi
- PDB-2onu: Plasmodium falciparum ubiquitin conjugating enzyme PF10_0330, put... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2onu
TitlePlasmodium falciparum ubiquitin conjugating enzyme PF10_0330, putative homologue of human UBE2H
ComponentsUbiquitin-conjugating enzyme, putative
KeywordsLIGASE / Ubiquitin-conjugating enzyme / UBC / Ubiquitin / Plasmodium falciparum / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / E2 ubiquitin-conjugating enzyme / acyltransferase activity / ubiquitin conjugating enzyme activity / protein polyubiquitination / ubiquitin-protein transferase activity / ubiquitin-dependent protein catabolic process / ATP binding / nucleus
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2, putative
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsDong, A. / Lew, J. / Lin, L. / Hassanali, A. / Zhao, Y. / Senisterra, G. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Bochkarev, A. ...Dong, A. / Lew, J. / Lin, L. / Hassanali, A. / Zhao, Y. / Senisterra, G. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Hui, R. / Brokx, S.J. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Plasmodium falciparum ubiquitin conjugating enzyme PF10_0330, putative homologue of human UBE2H
Authors: Dong, A. / Lew, J. / Lin, L. / Hassanali, A. / Zhao, Y. / Senisterra, G. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / ...Authors: Dong, A. / Lew, J. / Lin, L. / Hassanali, A. / Zhao, Y. / Senisterra, G. / Wasney, G. / Vedadi, M. / Kozieradzki, I. / Bochkarev, A. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Hui, R. / Brokx, S.J.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3122
Polymers17,1171
Non-polymers1941
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.821, 52.821, 206.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Ubiquitin-conjugating enzyme, putative /


Mass: 17117.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF10_0330 / Plasmid: p15-tev-lic DERIVED FROM PET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta-R3 / References: UniProt: Q8IJ70, ubiquitin-protein ligase
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 17, 2007 / Details: VeriMax HR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 12626 / Num. obs: 12626 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 7.5
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 2.41 / Num. unique all: 623 / Rsym value: 0.961 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YH6

1yh6
PDB Unreleased entry


Resolution: 2.38→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.095 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.231 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PROGRAM COOT 0.1.2 HAS ALSO BEEN USED IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.24978 608 4.8 %RANDOM
Rwork0.21349 ---
all0.21528 0 --
obs0.21528 11957 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.566 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20 Å20 Å2
2--1.93 Å20 Å2
3----3.86 Å2
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 13 122 1318
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221228
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9721671
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0155149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.10125.74154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8615193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.099151
X-RAY DIFFRACTIONr_chiral_restr0.1010.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02930
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.2555
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8961.5773
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51821217
X-RAY DIFFRACTIONr_scbond_it2.0753529
X-RAY DIFFRACTIONr_scangle_it3.2494.5454
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 60 -
Rwork0.258 828 -
obs--99.33 %

+
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