6MC0

Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate

• PDB DOI: https://doi.org/10.2210/pdb6MC0/pdb

• Classification: ISOMERASE
• Organism(s): Legionella pneumophila subsp. pneumophila str. Philadelphia 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-08-30 Released: 2018-09-12 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.154 
• R-Value Observed: 0.158 

Starting Model: experimental

Literature

Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila with Bound Substrate Ribose-5-Phosphate and Product Ribulose-5-Phosphate

Braverman, K.N., Dranow, D.M., Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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: 48.66 kDa 
• Atom Count: 3,758 
• Modelled Residue Count: 435 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-5-phosphate isomerase A	A, B	224	Legionella pneumophila subsp. pneumophila str. Philadelphia 1	Mutation(s): 0  Gene Names: rpiA, lpg0094 EC: 5.3.1.6
UniProt
Find proteins for Q5ZZB7 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)) Explore Q5ZZB7  Go to UniProtKB:  Q5ZZB7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RP	E [auth B]	RIBULOSE-5-PHOSPHATE C5 H11 O8 P FNZLKVNUWIIPSJ-UHNVWZDZSA-N
R5P	C [auth A]	RIBOSE-5-PHOSPHATE C5 H11 O8 P PPQRONHOSHZGFQ-LMVFSUKVSA-N
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.203 
• R-Value Work: 0.154 
• R-Value Observed: 0.158 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/m36mc0

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.29	α = 90
b = 67.56	β = 118.82
c = 73.32	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description