4EMY | pdb_00004emy

Crystal structure of aminotransferase from anaerococcus prevotii dsm 20548.

• PDB DOI: https://doi.org/10.2210/pdb4EMY/pdb
• Entry: 4EMY supersedes: 3T18

• Classification: TRANSFERASE
• Organism(s): Anaerococcus prevotii DSM 20548
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-12 Released: 2012-05-09 
• Deposition Author(s): Chang, C., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free: 
  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Literature

Crystal structure of aminotransferase from anaerococcus prevotii dsm 20548.

Chang, C., Tesar, C., Bearden, J., Joachimiak, A.

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: 188.06 kDa 
• Atom Count: 13,055 
• Modeled Residue Count: 1,632 
• Deposited Residue Count: 1,652 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase class I and II	A, B, C, D	413	Anaerococcus prevotii DSM 20548	Mutation(s): 0  Gene Names: Apre_1502
UniProt
Find proteins for C7REB0 (Anaerococcus prevotii (strain ATCC 9321 / DSM 20548 / JCM 6508 / NCTC 11806 / PC1)) Explore C7REB0  Go to UniProtKB:  C7REB0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.86 Å
• R-Value Free:  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34EMY

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.297	α = 90
b = 131.178	β = 90
c = 239.913	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXDE	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-09 
Deposition Author(s): Chang, C., Tesar, C., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 3T18

Revision History  

• Version 1.0: 2012-05-09
  Type: Initial release
  
• Version 1.1: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary