2ZSM

Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix, hexagonal form

• PDB DOI: https://doi.org/10.2210/pdb2ZSM/pdb

• Classification: ISOMERASE
• Organism(s): Aeropyrum pernix
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-17 Released: 2008-10-21 
• Deposition Author(s): Mizutani, H., Kunishima, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 

Literature

Crystal structure of glutamate-1-semialdehyde 2,1-aminomutase from Aeropyrum pernix

Mizutani, H., Kunishima, N.

To be published.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 140.44 kDa 
• Atom Count: 10,367 
• Modelled Residue Count: 1,263 
• Deposited Residue Count: 1,302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate-1-semialdehyde 2,1-aminomutase	A, B, C	434	Aeropyrum pernix	Mutation(s): 0  EC: 5.4.3.8
UniProt
Find proteins for Q9Y9I9 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9Y9I9  Go to UniProtKB:  Q9Y9I9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PMP	D [auth A], F [auth B], H [auth C]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N
CL	E [auth A], G [auth B], I [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.211 
• R-Value Work: 0.176 
• R-Value Observed: 0.176 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.39	α = 90
b = 123.39	β = 90
c = 356.443	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-21 
Deposition Author(s): Mizutani, H., Kunishima, N.

Revision History  

• Version 1.0: 2008-10-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description