3GJY | pdb_00003gjy

Crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032

• PDB DOI: https://doi.org/10.2210/pdb3GJY/pdb

• Classification: TRANSFERASE
• Organism(s): Corynebacterium glutamicum ATCC 13032
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-09 Released: 2009-03-24 
• Deposition Author(s): Tan, K., Li, H., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 
  0.192 (Depositor), 0.187 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

The crystal structure of a probable spermidine synthase from Corynebacterium glutamicum ATCC 13032.

Tan, K., Li, H., Freeman, L., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.26 kDa 
• Atom Count: 2,639 
• Modeled Residue Count: 279 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spermidine synthase	A	317	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0  Gene Names: Cgl1237, cg1394
UniProt
Find proteins for Q8NR27 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q8NR27  Go to UniProtKB:  Q8NR27

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free:  0.192 (Depositor), 0.187 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.909	α = 90
b = 65.009	β = 90
c = 87.308	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP/wARP	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Tan, K., Li, H., Freeman, L., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary