3PSM | pdb_00003psm

.98A crystal structure of a dimeric plant defensin SPE10

• PDB DOI: https://doi.org/10.2210/pdb3PSM/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Pachyrhizus erosus
• Mutation(s): No 


• Deposited: 2010-12-01 Released: 2010-12-29 
• Deposition Author(s): Zhou, H., Song, X., Gong, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free: 
  0.164 (Depositor) 
• R-Value Work: 
  0.120 (Depositor) 
• R-Value Observed: 
  0.125 (Depositor) 

Literature

0.98A crystal structure of a dimeric plant defensin SPE10

Zhou, H., Song, X., Gong, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 11.02 kDa 
• Atom Count: 955 
• Modeled Residue Count: 94 
• Deposited Residue Count: 94 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Defensin	A, B	47	Pachyrhizus erosus	Mutation(s): 0
UniProt
Find proteins for Q6B519 (Pachyrhizus erosus) Explore Q6B519  Go to UniProtKB:  Q6B519

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.98 Å
• R-Value Free:  0.164 (Depositor) 
• R-Value Work:  0.120 (Depositor) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.714	α = 90
b = 28.111	β = 103.78
c = 54.853	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
Shake	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
Shake	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Zhou, H., Song, X., Gong, W.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Structure summary