4IR8 | pdb_00004ir8

1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bisphosphatase from Toxoplasma gondii

• PDB DOI: https://doi.org/10.2210/pdb4IR8/pdb
• Entry: 4IR8 supersedes: 3UKS

• Classification: HYDROLASE
• Organism(s): Toxoplasma gondii ME49
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-14 Released: 2013-01-23 
• Deposition Author(s): Minasov, G., Ruan, J., Wawrzak, Z., Halavaty, A., Shuvalova, L., Harb, O.S., Ngo, H., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.185 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.154 (Depositor) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

1.85 Angstrom Crystal Structure of Putative Sedoheptulose-1,7 bisphosphatase from Toxoplasma gondii.

Minasov, G., Ruan, J., Wawrzak, Z., Halavaty, A., Shuvalova, L., Harb, O.S., Ngo, H., Anderson, W.F., 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)

Macromolecule Content 

• Total Structure Weight: 76.19 kDa 
• Atom Count: 5,832 
• Modeled Residue Count: 634 
• Deposited Residue Count: 694 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sedoheptulose-1,7 bisphosphatase, putative	A, B	347	Toxoplasma gondii ME49	Mutation(s): 0  Gene Names: TGGT1_070070, TGME49_035700, TGVEG_061570 EC: 3.1.3.37
UniProt
Find proteins for B9PW60 (Toxoplasma gondii (strain ATCC 50861 / VEG)) Explore B9PW60  Go to UniProtKB:  B9PW60

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A], D [auth A], E [auth B], F [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT	G [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.185 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.154 (Depositor) 
• R-Value Observed: 0.156 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34ir8

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.4	α = 90
b = 64.4	β = 90
c = 591.61	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-23 
Deposition Author(s): Minasov, G., Ruan, J., Wawrzak, Z., Halavaty, A., Shuvalova, L., Harb, O.S., Ngo, H., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3UKS

Revision History  

• Version 1.0: 2013-01-23
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description