8GZI

Crystal Structure of ApiI in complex with SAH

• PDB DOI: https://doi.org/10.2210/pdb8GZI/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Apiospora montagnei NRRL 25634
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-27 Released: 2023-09-27 
• Deposition Author(s): Zhou, J.H., Lu, J.Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Literature

Crystal Structure of ApiI in complex with SAH

Zhou, J.H., Lu, J.Y.

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)

Macromolecule Content

• Total Structure Weight: 44.22 kDa 
• Atom Count: 3,062 
• Modelled Residue Count: 382 
• Deposited Residue Count: 407 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ApiI	A	407	Apiospora montagnei NRRL 25634	Mutation(s): 0
UniProt
Find proteins for A0A9Y2YAB6 (Apiospora montagnei NRRL 25634) Explore A0A9Y2YAB6  Go to UniProtKB:  A0A9Y2YAB6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH (Subject of Investigation/LOI)	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.024	α = 90
b = 98.024	β = 90
c = 80.257	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-27 
Deposition Author(s): Zhou, J.H., Lu, J.Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	91856202

Revision History  

• Version 1.0: 2023-09-27
  Type: Initial release