6J03 | pdb_00006j03

Crystal structure of a cyclase mutant in apo form

• PDB DOI: https://doi.org/10.2210/pdb6J03/pdb

• Classification: TRANSFERASE
• Organism(s): Fischerella ambigua UTEX 1903
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-12-20 Released: 2019-12-25 
• Deposition Author(s): Tang, X.K., Liu, W.D., Chen, C.C., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.140 (Depositor), 0.142 (DCC) 
• R-Value Work: 
  0.108 (Depositor), 0.113 (DCC) 
• R-Value Observed: 
  0.110 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the calcium dependence of Stig cyclases.

Tang, X.K., Xue, J., Yang, Y.Y., Ko, T.P., Chen, C.Y., Dai, L.H., Guo, R.T., Zhang, Y.H., Chen, C.C.

(2019) RSC Adv 9: 13182-13185

• DOI: https://doi.org/10.1039/C9RA00960D

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: 22.04 kDa 
• Atom Count: 1,915 
• Modeled Residue Count: 200 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-epi-hapalindole U synthase	A	200	Fischerella ambigua UTEX 1903	Mutation(s): 2
UniProt
Find proteins for V5TER4 (Fischerella ambigua (strain UTEX 1903)) Explore V5TER4  Go to UniProtKB:  V5TER4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0HZ (Subject of Investigation/LOI)	B [auth A]	amino({3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}amino)methaniminium C11 H20 N5 O2 ZRJHYOXNWCMGMW-JGVFFNPUSA-O
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.140 (Depositor), 0.142 (DCC) 
• R-Value Work:  0.108 (Depositor), 0.113 (DCC) 
• R-Value Observed: 0.110 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.779	α = 90
b = 54.779	β = 90
c = 152.416	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-25 
Deposition Author(s): Tang, X.K., Liu, W.D., Chen, C.C., Guo, R.T.

Revision History  

• Version 1.0: 2019-12-25
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description