1VJO | pdb_00001vjo

Crystal structure of Alanine--glyoxylate aminotransferase (ALR1004) from Nostoc sp. at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VJO/pdb

• Classification: TRANSFERASE
• Organism(s): Nostoc sp. PCC 7120 = FACHB-418
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-03-16 Released: 2004-03-23 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.202 (Depositor), 0.162 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor

Han, G.W., Schwarzenbacher, R., Page, R., Jaroszewski, L., Abdubek, P., Ambing, E., Biorac, T., Canaves, J.M., Chiu, H.J., Dai, X., Deacon, A.M., DiDonato, M., Elsliger, M.A., Godzik, A., Grittini, C., Grzechnik, S.K., Hale, J., Hampton, E., Haugen, J., Hornsby, M., Klock, H.E., Koesema, E., Kreusch, A., Kuhn, P., Lesley, S.A., Levin, I., McMullan, D., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Nigoghossian, E., Ouyang, J., Paulsen, J., Quijano, K., Reyes, R., Sims, E., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., von Delft, F., Wang, X., West, B., White, A., Wolf, G., Xu, Q., Zagnitko, O., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2005) Proteins 58: 971-975

• PubMed: 15657930 
• DOI: https://doi.org/10.1002/prot.20360
• Primary Citation of Related Structures:  
  1VJO

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Organizational Affiliation: 
• The Joint Center for Structural Genomics, The Scripps Research Institute, La Jolla, CA 92037, USA.

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 44 kDa 
• Atom Count: 3,369 
• Modeled Residue Count: 377 
• Deposited Residue Count: 393 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alanine--glyoxylate aminotransferase	A	393	Nostoc sp. PCC 7120 = FACHB-418	Mutation(s): 8  EC: 2.6.1.44

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-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: 1.70 Å
• R-Value Free:  0.202 (Depositor), 0.162 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VJO

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.258	α = 90
b = 101.057	β = 90
c = 97.252	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
SHELXD	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-23 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-03-23
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations