1N5B | pdb_00001n5b

Crystal Structure Of The Yersinia enterocolitica Molecular Chaperone Syce

• PDB DOI: https://doi.org/10.2210/pdb1N5B/pdb
• Entry: 1N5B supersedes: 1MD1

• Classification: CHAPERONE
• Organism(s): Yersinia enterocolitica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-11-05 Released: 2002-11-20 
• Deposition Author(s): Trame, C.B., McKay, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.290 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.248 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.248 (Depositor) 

Starting Model: experimental

Literature

Structure of the Yersinia enterocolitica molecular-chaperone protein SycE.

Trame, C.B., McKay, D.B.

(2003) Acta Crystallogr D Biol Crystallogr 59: 389-392

• PubMed: 12554962 
• DOI: https://doi.org/10.1107/s0907444902020826
• Primary Citation Related Structures: 
  1N5B


• PubMed Abstract: 
  

  The crystal structure of the Yersinia enterocolitica molecular-chaperone protein SycE, which specifically binds the YopE protein, has been solved to 2.0 A resolution by molecular replacement. The crystal contains two SycE dimers per asymmetric unit; a novel feature of this crystal, when compared with closely related SycE structures, is a well ordered carboxy-terminal peptide in one protomer of each dimer. The peptide binds a hydrophobic patch of a neighboring molecule in a manner similar to that seen in a SycE-YopE chaperone-target complex, suggestive of low-affinity 'self-binding' through which the carboxy-terminal peptide might suppress counterproductive interactions with non-target proteins in vivo.

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Organizational Affiliation: 
• Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.36 kDa 
• Atom Count: 4,039 
• Modeled Residue Count: 497 
• Deposited Residue Count: 528 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YOPE regulator	A, B, C, D	132	Yersinia enterocolitica	Mutation(s): 0  Gene Names: YERA
UniProt
Find proteins for P31490 (Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)) Explore P31490  Go to UniProtKB:  P31490

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.290 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.248 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.248 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.55	α = 90
b = 92.67	β = 90
c = 101.05	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-11-20 
Deposition Author(s): Trame, C.B., McKay, D.B.
• This entry supersedes: 1MD1

Revision History  

• Version 1.0: 2002-11-20
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Refinement description