2ONU | pdb_00002onu

Plasmodium falciparum ubiquitin conjugating enzyme PF10_0330, putative homologue of human UBE2H

PDB DOI: https://doi.org/10.2210/pdb2ONU/pdb

Classification: LIGASE
Organism(s): Plasmodium falciparum 3D7
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-01-24 Released: 2007-02-06
Deposition Author(s): 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.250 (Depositor), 0.249 (DCC)
R-Value Work:
0.213 (Depositor), 0.211 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Plasmodium falciparum ubiquitin conjugating enzyme PF10_0330, putative homologue of human UBE2H

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.

To be published.

Macromolecule Content

Total Structure Weight: 17.31 kDa
Atom Count: 1,318
Modeled Residue Count: 150
Deposited Residue Count: 152
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme, putative	A	152	Plasmodium falciparum 3D7	Mutation(s): 0 Gene Names: PF10_0330 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt
Find proteins for Q8IJ70 (Plasmodium falciparum (isolate 3D7)) Explore Q8IJ70 Go to UniProtKB: Q8IJ70
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8IJ70
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.250 (Depositor), 0.249 (DCC)
R-Value Work: 0.213 (Depositor), 0.211 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.821	α = 90
b = 52.821	β = 90
c = 206.886	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-02-06

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-02-06
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description