3L9Y

Crystal structures of holo and Cu-deficient Cu/ZnSOD from the silkworm Bombyx mori and the implications in Amyotrophic lateral sclerosis

• PDB DOI: https://doi.org/10.2210/pdb3L9Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-01-06 Released: 2010-03-23 
• Deposition Author(s): Zhang, N.-N., He, Y.-X., Li, W.-F., Zhao, F., Yan, L.-F., Zhang, G.-Z., Teng, Y.-B., Yu, J., Chen, Y., Zhou, C.-Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Starting Model: experimental

Literature

Crystal structures of holo and Cu-deficient Cu/Zn-SOD from the silkworm Bombyx mori and the implications in amyotrophic lateral sclerosis.

Zhang, N.N., He, Y.X., Li, W.F., Teng, Y.B., Yu, J., Chen, Y., Zhou, C.Z.

(2010) Proteins 78: 1999-2004

• PubMed: 20310068 
• DOI: https://doi.org/10.1002/prot.22709
• Primary Citation of Related Structures:  
  3L9E, 3L9Y

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Anhui, People's Republic of China.

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 (software)

Macromolecule Content

• Total Structure Weight: 31.9 kDa 
• Atom Count: 2,367 
• Modelled Residue Count: 307 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Superoxide dismutase [Cu-Zn]	A, B	154	Bombyx mori	Mutation(s): 2  Gene Names: SOD1 EC: 1.15.1.1
UniProt
Find proteins for P82205 (Bombyx mori) Explore P82205  Go to UniProtKB:  P82205

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	D [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.258 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 6₄

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.493	α = 90
b = 111.493	β = 90
c = 39.886	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Zhang, N.-N., He, Y.-X., Li, W.-F., Zhao, F., Yan, L.-F., Zhang, G.-Z., Teng, Y.-B., Yu, J., Chen, Y., Zhou, C.-Z.

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-12-25
  Changes: Database references
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-11-01
  Changes: Data collection, Refinement description
• Version 1.6: 2024-11-13
  Changes: Structure summary