4M8L | pdb_00004m8l

crystal structure of RpiA-R5P complex

• PDB DOI: https://doi.org/10.2210/pdb4M8L/pdb

• Classification: ISOMERASE
• Organism(s): Francisella tularensis
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2013-08-13 Released: 2013-10-02 
• Deposition Author(s): Rostankowski, R., Borek, D., Orlikowska, M., Nakka, C., Grimshaw, S., Otwinowski, Z., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

Literature

crystal structure of RpiA-R5P complex

Rostankowski, R., Borek, D., Orlikowska, M., Nakka, C., Grimshaw, S., Otwinowski, Z., Center for Structural Genomics of Infectious Diseases (CSGID)

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 100.92 kDa 
• Atom Count: 7,188 
• Modeled Residue Count: 872 
• Deposited Residue Count: 896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose-5-phosphate isomerase A	A, B, C, D	224	Francisella tularensis	Mutation(s): 0  Gene Names: rpiA, FTW_1255 EC: 5.3.1.6
UniProt
Find proteins for A4IYN5 (Francisella tularensis subsp. tularensis (strain WY96-3418)) Explore A4IYN5  Go to UniProtKB:  A4IYN5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5RP	E [auth A], MA [auth C], V [auth B], ZA [auth D]	RIBULOSE-5-PHOSPHATE C5 H11 O8 P FNZLKVNUWIIPSJ-UHNVWZDZSA-N
ARF	AA [auth B], AB [auth D], BA [auth B], BB [auth D], CA [auth B], DA [auth B], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], QA [auth C], R [auth A], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], UA [auth C], VA [auth C], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], Z [auth B]	FORMAMIDE C H3 N O ZHNUHDYFZUAESO-UHFFFAOYSA-N
CL	JA [auth B], KA [auth B], LA [auth B], U [auth A], YA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.274 (Depositor), 0.278 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.203	α = 90
b = 151.958	β = 93.98
c = 36.29	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-02 
Deposition Author(s): Rostankowski, R., Borek, D., Orlikowska, M., Nakka, C., Grimshaw, S., Otwinowski, Z., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2013-10-02
  Type: Initial release
  
• Version 1.1: 2013-10-09
  Changes: Other
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description