6ZEA | pdb_00006zea

Strictosidine Synthase from Catharanthus roseus in complex with racemic 1-methyl-2,3,4,9-tetrahydro-1H-beta-carboline

• PDB DOI: https://doi.org/10.2210/pdb6ZEA/pdb

• Classification: LYASE
• Organism(s): Catharanthus roseus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-06-16 Released: 2020-09-02 
• Deposition Author(s): Eger, E., Sharma, M., Kroutil, W., Grogan, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 
  0.218 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Strictosidine Synthase from Catharanthus roseus in complex with racemic 1-methyl-2,3,4,9-tetrahydro-1H-beta-carboline

Eger, E., Sharma, M., Kroutil, W., Grogan, G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 36.38 kDa 
• Atom Count: 2,685 
• Modeled Residue Count: 308 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Strictosidine synthase	A	321	Catharanthus roseus	Mutation(s): 0  Gene Names: STR1, SSS EC: 4.3.3.2 (PDB Primary Data), 3.5.99.13 (UniProt)
UniProt
Find proteins for P18417 (Catharanthus roseus) Explore P18417  Go to UniProtKB:  P18417

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QGH (Subject of Investigation/LOI)	F [auth A]	(1~{R})-1-methyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole C12 H14 N2 LPIJOZBIVDCQTE-MRVPVSSYSA-N
QGK (Subject of Investigation/LOI)	G [auth A]	(1~{S})-1-methyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole C12 H14 N2 LPIJOZBIVDCQTE-QMMMGPOBSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free:  0.218 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.44	α = 90
b = 71.42	β = 90
c = 109.58	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-02 
Deposition Author(s): Eger, E., Sharma, M., Kroutil, W., Grogan, G.

Revision History  

• Version 1.0: 2020-09-02
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary