5IBX

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb5IBX/pdb

• Classification: ISOMERASE
• Organism(s): Streptococcus pneumoniae D39
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-22 Released: 2016-03-09 
• Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.232 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

1.65 Angstrom Crystal Structure of Triosephosphate Isomerase (TIM) from Streptococcus pneumoniae

Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 215.46 kDa 
• Atom Count: 17,739 
• Modelled Residue Count: 1,999 
• Deposited Residue Count: 2,040 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, D, E, H	255	Streptococcus pneumoniae D39	Mutation(s): 0  Gene Names: tpiA, SPD_1404 EC: 5.3.1.1
UniProt
Find proteins for Q04JH4 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04JH4  Go to UniProtKB:  Q04JH4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	C, F, G	255	Streptococcus pneumoniae D39	Mutation(s): 0  Gene Names: tpiA, SPD_1404 EC: 5.3.1.1
UniProt
Find proteins for Q04JH4 (Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)) Explore Q04JH4  Go to UniProtKB:  Q04JH4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	I [auth A], J [auth B], K [auth B], L [auth C], M [auth C], N [auth C], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth F], T [auth G], U [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B, D, E, H	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.232 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m35ibx

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.845	α = 75.43
b = 84.351	β = 65.97
c = 92.463	γ = 62.03

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Flores, K., Shatsman, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description