2GUP | pdb_00002gup

Structural Genomics, the crystal structure of a ROK family protein from Streptococcus pneumoniae TIGR4 in complex with sucrose

• PDB DOI: https://doi.org/10.2210/pdb2GUP/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-05-01 Released: 2006-05-30 
• Deposition Author(s): Tan, K., Li, H., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

The crystal structure of a ROK family protein from Streptococcus pneumoniae TIGR4 in complex with sucrose

Tan, K., Li, H., Abdullah, J., 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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 33.15 kDa 
• Atom Count: 2,372 
• Modeled Residue Count: 289 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ROK family protein	A	292	Streptococcus pneumoniae TIGR4	Mutation(s): 6
UniProt
Find proteins for A0A0H2USG4 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2USG4  Go to UniProtKB:  A0A0H2USG4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B, C, D	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	B, C, D	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free:  0.228 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.678	α = 90
b = 114.665	β = 90
c = 117.677	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data scaling
HKL-3000	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-30 
Deposition Author(s): Tan, K., Li, H., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2006-05-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary