3QAC | pdb_00003qac

Structure of amaranth 11S proglobulin seed storage protein from Amaranthus hypochondriacus L.

• PDB DOI: https://doi.org/10.2210/pdb3QAC/pdb

• Classification: PLANT PROTEIN
• Organism(s): Amaranthus hypochondriacus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-10 Released: 2012-01-11 
• Deposition Author(s): Tandang-Silvas, M.R., Carrazco-Pena, L., Barba de la Rosa, A.P., Osuna-Castro, J.A., Utsumi, S., Mikami, B., Maruyama, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.249 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Structure of amaranth 11S proglobulin, a major seed storage protein from Amaranthus hypochondriacus L.

Tandang-Silvas, M.R., Carrazco-Pena, L., Barba de la Rosa, A.P., Osuna-Castro, J.A., Utsumi, S., Mikami, B., Maruyama, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.72 kDa 
• Atom Count: 3,027 
• Modeled Residue Count: 372 
• Deposited Residue Count: 465 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
11S globulin seed storage protein	A	465	Amaranthus hypochondriacus	Mutation(s): 0
UniProt
Find proteins for Q38712 (Amaranthus hypochondriacus) Explore Q38712  Go to UniProtKB:  Q38712

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.249 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.077	α = 90
b = 94.077	β = 90
c = 74.67	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-11 
Deposition Author(s): Tandang-Silvas, M.R., Carrazco-Pena, L., Barba de la Rosa, A.P., Osuna-Castro, J.A., Utsumi, S., Mikami, B., Maruyama, N.

Revision History  

• Version 1.0: 2012-01-11
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary