3KPA | pdb_00003kpa

Ubiquitin fold modifier conjugating enzyme from Leishmania major (probable)

• PDB DOI: https://doi.org/10.2210/pdb3KPA/pdb

• Classification: LIGASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2009-11-16 Released: 2009-12-01 
• Deposition Author(s): Han, G.W., Le Trong, I., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Ubiquitin fold modifier conjugating enzyme from Leishmania major (probable)

Merritt, E.A., Le Trong, I., Han, G.W., Anderson, L., Napuli, A., Van Voorhis, W.C., Buckner, F.S., Fan, E., Zucker, F., Verlinde, L.M.J., Hol, W.G.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.43 kDa 
• Atom Count: 3,872 
• Modeled Residue Count: 471 
• Deposited Residue Count: 504 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
probable Ubiquitin fold modifier conjugating enzyme	A, B, C	168	Leishmania major	Mutation(s): 1  Gene Names: LmjF15.1250
UniProt
Find proteins for Q4QF57 (Leishmania major) Explore Q4QF57  Go to UniProtKB:  Q4QF57

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.273 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.274	α = 90
b = 34.133	β = 99.32
c = 126.774	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Han, G.W., Le Trong, I., Merritt, E.A., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2023-11-22
  Changes: Data collection
• Version 1.6: 2024-11-27
  Changes: Structure summary