4RVP | pdb_00004rvp

Crystal structure of superoxide dismutase from sedum alfredii

• PDB DOI: https://doi.org/10.2210/pdb4RVP/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sedum alfredii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-27 Released: 2015-12-16 
• Deposition Author(s): Qiu, R., Li, C., Zhai, J., Tang, L., Zhang, H., Yuan, M., Hu, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.290 (Depositor), 0.294 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.227 (Depositor) 

Starting Model: experimental

Literature

The positive effects of Cd and Cd-Zn relationship in the Zn-related physiological processes involved in growth in the Zn/Cd hyperaccumulator Sedum alfredii

Qiu, R., Li, C., Zhai, J., Tang, L., Zhang, H., Yuan, M., Hu, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 97.15 kDa 
• Atom Count: 6,704 
• Modeled Residue Count: 923 
• Deposited Residue Count: 948 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
superoxide dismutase	A, B, C, D, E, F	158	Sedum alfredii	Mutation(s): 0  EC: 1.15.1.1
UniProt
Find proteins for A0A0A0QA66 (Sedum alfredii) Explore A0A0A0QA66  Go to UniProtKB:  A0A0A0QA66

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.290 (Depositor), 0.294 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.979	α = 90
b = 85.781	β = 99.84
c = 105.312	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
PHENIX	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Qiu, R., Li, C., Zhai, J., Tang, L., Zhang, H., Yuan, M., Hu, X.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-27
  Changes: Structure summary