8R39 | pdb_00008r39

Full-length LpMIP mutant Y16F

• PDB DOI: https://doi.org/10.2210/pdb8R39/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-11-08 Released: 2024-11-20 
• Deposition Author(s): Whittaker, J.J., Guskov, A.
• Funding Organization(s): German Research Foundation (DFG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.271 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Full-length LpMIP mutant Y16F

Whittaker, J.J., Guskov, 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 (software)

Biological Assembly Evidence: NMR relaxation study

Macromolecule Content 

• Total Structure Weight: 23.1 kDa 
• Atom Count: 1,681 
• Modeled Residue Count: 208 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A [auth C]	208	Legionella pneumophila	Mutation(s): 1  Gene Names: C3927_03235 EC: 5.2.1.8
UniProt
Find proteins for A5IGB8 (Legionella pneumophila (strain Corby)) Explore A5IGB8  Go to UniProtKB:  A5IGB8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth C]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
PEG	E [auth C], F [auth C]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	B [auth C], C, G [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.271 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.444	α = 90
b = 78.444	β = 90
c = 105.176	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Whittaker, J.J., Guskov, A.

---

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	390713860

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release