1J4G | pdb_00001j4g

crystal structure analysis of the trichosanthin delta C7

• PDB DOI: https://doi.org/10.2210/pdb1J4G/pdb

• Classification: HYDROLASE
• Organism(s): Trichosanthes kirilowii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-09-30 Released: 2001-10-24 
• Deposition Author(s): Ding, Y., Too, H.M., Wang, Z.L., Liu, Y.W., Dong, Y.C., Shaw, P.C., Rao, Z.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.174 (Depositor) 

Literature

crystal structure analysis of the trichosanthin delta C7

Ding, Y., Too, H.M., Wang, Z.L., Liu, Y.W., Dong, Y.C., Shaw, P.C., Rao, Z.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 109.35 kDa 
• Atom Count: 8,483 
• Modelled Residue Count: 964 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trichosanthin delta C7	A, B, C, D	248	Trichosanthes kirilowii	Mutation(s): 0  EC: 3.2.2.22
UniProt
Find proteins for P09989 (Trichosanthes kirilowii) Explore P09989  Go to UniProtKB:  P09989

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.174 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.56	α = 90
b = 74.4	β = 96.96
c = 87.56	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-10-24 
Deposition Author(s): Ding, Y., Too, H.M., Wang, Z.L., Liu, Y.W., Dong, Y.C., Shaw, P.C., Rao, Z.H.

Revision History  

• Version 1.0: 2001-10-24
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection