3TV9 | pdb_00003tv9

Crystal Structure of Putative Peptide Maturation Protein from Shigella flexneri

• PDB DOI: https://doi.org/10.2210/pdb3TV9/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Shigella flexneri
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-09-19 Released: 2011-10-05 
• Deposition Author(s): Kim, Y., Maltseva, N., Gu, M., 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: 
  0.249 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal Structure of Putative Peptide Maturation Protein from

Kim, Y., Maltseva, N., Gu, M., Anderson, W.F., Joachimiak, A.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.41 kDa 
• Atom Count: 3,423 
• Modeled Residue Count: 436 
• Deposited Residue Count: 457 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative peptide maturation protein	A	457	Shigella flexneri	Mutation(s): 0  Gene Names: pmbA, S4517
UniProt
Find proteins for A0A0H2W186 (Shigella flexneri) Explore A0A0H2W186  Go to UniProtKB:  A0A0H2W186

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	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:  0.249 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33tv9

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.133	α = 90
b = 61.12	β = 90
c = 65.101	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Kim, Y., Maltseva, N., Gu, M., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary