3WE5 | pdb_00003we5

Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita

PDB DOI: https://doi.org/10.2210/pdb3WE5/pdb

Classification: LIGASE
Organism(s): Cyclocybe aegerita
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-07-01 Released: 2014-07-09
Deposition Author(s): Li, D.F., Feng, L., Wang, D.C., Liu, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.234 (Depositor), 0.232 (DCC)
R-Value Work:
0.202 (Depositor), 0.197 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of ubiquitin conjugating enzyme E2 UbcA1 from Agrocybe aegerita

Li, D.F., Feng, L., Wang, D.C., Liu, W.

To be published.

Macromolecule Content

Total Structure Weight: 38.48 kDa
Atom Count: 2,531
Modeled Residue Count: 282
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin conjugating enzyme	A, B	173	Cyclocybe aegerita	Mutation(s): 0 EC: 6.3.2.19
UniProt
Find proteins for H9CTH3 (Cyclocybe aegerita) Explore H9CTH3 Go to UniProtKB: H9CTH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	H9CTH3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.234 (Depositor), 0.232 (DCC)
R-Value Work: 0.202 (Depositor), 0.197 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.93	α = 90
b = 34.76	β = 108.88
c = 128.1	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.