3LM7 | pdb_00003lm7

Crystal Structure of DUF1341 representative, from Yersinia enterocolitica subsp. enterocolitica 8081

• PDB DOI: https://doi.org/10.2210/pdb3LM7/pdb

• Classification: LYASE
• Organism(s): Yersinia enterocolitica subsp. enterocolitica 8081
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-29 Released: 2010-02-23 
• Deposition Author(s): Joachimiak, A., Duke, N.E.C., Feldmann, B., Wu, R., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.192 (Depositor), 0.176 (DCC) 
• R-Value Work: 
  0.135 (Depositor) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

Crystal Structure of DUF1341 representative, from Yersinia enterocolitica subsp. enterocolitica 8081

Joachimiak, A., Duke, N.E.C., Feldmann, B., Wu, R.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 54.12 kDa 
• Atom Count: 4,448 
• Modeled Residue Count: 495 
• Deposited Residue Count: 498 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative 4-Hydroxy-2-oxoglutarate aldolase / 2-dehydro-3-deoxyphosphogluconate aldolase	A, B	249	Yersinia enterocolitica subsp. enterocolitica 8081	Mutation(s): 0  Gene Names: YE3779
UniProt
Find proteins for A1JRF3 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore A1JRF3  Go to UniProtKB:  A1JRF3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BR	C [auth A], D [auth B]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M
K	E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.192 (Depositor), 0.176 (DCC) 
• R-Value Work:  0.135 (Depositor) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.947	α = 90
b = 60.453	β = 90
c = 159.119	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Joachimiak, A., Duke, N.E.C., Feldmann, B., Wu, R., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary