1G2W | pdb_00001g2w

E177S MUTANT OF THE PYRIDOXAL-5'-PHOSPHATE ENZYME D-AMINO ACID AMINOTRANSFERASE

• PDB DOI: https://doi.org/10.2210/pdb1G2W/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-10-21 Released: 2000-11-15 
• Deposition Author(s): Lepore, B.W., Ringe, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.227 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Literature

Studies on an Active Site Residue, E177, That Affects Binding of the Coenzyme in D-Amino Acid Transaminase, and Mechanistic Studies on a Suicide Substrate

van Ophem, P.W., Lepore, B.W., Kishimoto, K., Ringe, D., Manning, J.M.

(2000) Biochemistry And Molecular Biology Of Vitamin B6 And Pqq-dependent Proteins, 10th Annual International Symposium On Vitamin B6 : 339-346

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)

Macromolecule Content 

• Total Structure Weight: 65.15 kDa 
• Atom Count: 4,701 
• Modeled Residue Count: 554 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ALANINE AMINOTRANSFERASE	A, B	282	Geobacillus stearothermophilus	Mutation(s): 1  EC: 2.6.1.21
UniProt
Find proteins for P19938 (Bacillus sp. (strain YM-1)) Explore P19938  Go to UniProtKB:  P19938

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.227 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.187	α = 90
b = 90.522	β = 90
c = 89.097	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-15 
Deposition Author(s): Lepore, B.W., Ringe, D.

Revision History  

• Version 1.0: 2000-11-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations