1K6Z | pdb_00001k6z

Crystal Structure of the Yersinia Secretion Chaperone SycE

• PDB DOI: https://doi.org/10.2210/pdb1K6Z/pdb

• Classification: CHAPERONE
• Organism(s): Yersinia pestis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-10-17 Released: 2001-10-31 
• Deposition Author(s): Evdokimov, A.G., Tropea, J.E., Routzahn, K.M., Waugh, D.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.248 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Three-dimensional structure of the type III secretion chaperone SycE from Yersinia pestis.

Evdokimov, A.G., Tropea, J.E., Routzahn, K.M., Waugh, D.S.

(2002) Acta Crystallogr D Biol Crystallogr 58: 398-406

• PubMed: 11856824 
• DOI: https://doi.org/10.1107/s090744490200015x
• Primary Citation Related Structures: 
  1K6Z


• PubMed Abstract: 
  

  Many bacterial pathogens utilize a type III (contact-dependent) secretion system to inject cytotoxic effector proteins directly into host cells. This ingenious mechanism, designed for both bacterial offense and defense, has been studied most extensively in Yersinia spp. To be exported efficiently, at least three of the effectors (YopE, YopH and YopT) and several other proteins that transit the type III secretion pathway in Yersinia (YopN, YopD and YopB) must first form transient complexes with cognate-specific Yop chaperone (Syc) proteins. The cytotoxic effector YopE, a selective activator of mammalian Rho-family GTPases, associates with SycE. Here, the structure of Y. pestis SycE at 1.95A resolution is reported. SycE possesses a novel fold with an unusual dimerization motif and an intriguing basic cavity located on the dyad axis of the dimer that may participate in its interaction with YopE.

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Organizational Affiliation: 
• Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, PO Box B, Frederick, MD 21702-1201, 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)

Macromolecule Content 

• Total Structure Weight: 32.7 kDa 
• Atom Count: 2,161 
• Modeled Residue Count: 243 
• Deposited Residue Count: 282 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III secretion chaperone SycE	A, B	141	Yersinia pestis	Mutation(s): 3  Gene Names: SycE
UniProt
Find proteins for P31491 (Yersinia pestis) Explore P31491  Go to UniProtKB:  P31491

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	C [auth A], D [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

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: 2.00 Å
• R-Value Free:  0.248 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.197 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.879	α = 90
b = 56.038	β = 114.04
c = 54.993	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
SHARP	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-31 
Deposition Author(s): Evdokimov, A.G., Tropea, J.E., Routzahn, K.M., Waugh, D.S.

Revision History  

• Version 1.0: 2001-10-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations, Refinement description
• Version 1.4: 2024-04-03
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-20
  Changes: Structure summary