1VJO | pdb_00001vjo

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

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) 

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This is version 1.3 of the entry. See complete history. 


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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
alanine--glyoxylate aminotransferase393Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 8 
EC: 2.6.1.44
UniProt
Find proteins for Q8YY48 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore Q8YY48 
Go to UniProtKB:  Q8YY48
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8YY48
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP
Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.258α = 90
b = 101.057β = 90
c = 97.252γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SHELXDphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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