4LKB | pdb_00004lkb

Crystal structure of a putative 4-Oxalocrotonate Tautomerase from Nostoc sp. PCC 7120

• PDB DOI: https://doi.org/10.2210/pdb4LKB/pdb

• Classification: ISOMERASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-07-07 Released: 2013-07-24 
• Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 
  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Crystal structure of a putative 4-Oxalocrotonate Tautomerase from Nostoc sp. PCC 7120

Kumaran, D., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 108.33 kDa 
• Atom Count: 6,348 
• Modeled Residue Count: 726 
• Deposited Residue Count: 906 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein alr4568/putative 4-Oxalocrotonate Tautomerase	A [auth F], B, C, D, E, F [auth A]	151	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 0  Gene Names: alr4568
UniProt
Find proteins for Q8YNJ7 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore Q8YNJ7  Go to UniProtKB:  Q8YNJ7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth F], I [auth B], L [auth D], M [auth D], O [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth F], J [auth C], K [auth D], N [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth F], B, C, D, E, F [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free:  0.221 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.022	α = 90
b = 132.926	β = 90
c = 133.121	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
SHELXE	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-24 
Deposition Author(s): Kumaran, D., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Seidel, R., Villigas, G., Zencheck, W., Al Obaidi, N., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2013-07-24
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary