4R40 | pdb_00004r40

Crystal Structure of TolB/Pal complex from Yersinia pestis.

• PDB DOI: https://doi.org/10.2210/pdb4R40/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-08-18 Released: 2014-09-03 
• Deposition Author(s): Maltseva, N., Kim, Y., Osipiuk, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.214 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of TolB/Pal complex from Yersinia pestis.

Maltseva, N., Kim, Y., Osipiuk, J., Anderson, W.F., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 119.95 kDa 
• Atom Count: 8,156 
• Modeled Residue Count: 1,059 
• Deposited Residue Count: 1,104 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein TolB	A, C	411	Yersinia pestis CO92	Mutation(s): 0  Gene Names: tolB, y3055, YPO1124, YP_1032
UniProt
Find proteins for Q8ZGZ1 (Yersinia pestis) Explore Q8ZGZ1  Go to UniProtKB:  Q8ZGZ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan-associated lipoprotein	B, D	141	Yersinia pestis CO92	Mutation(s): 0  Gene Names: excC, pal, y3054, YPO1125, YP_1031
UniProt
Find proteins for A0A2U2GZX0 (Yersinia pestis) Explore A0A2U2GZX0  Go to UniProtKB:  A0A2U2GZX0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], J [auth B], L [auth C], M [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth B], I [auth B], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
FMT	F [auth A], G [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.214 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.389	α = 90
b = 175.252	β = 89.83
c = 66.268	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-03 
Deposition Author(s): Maltseva, N., Kim, Y., Osipiuk, J., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2014-09-03
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2023-12-06
  Changes: Data collection
• Version 1.3: 2024-11-27
  Changes: Structure summary