3L9Y | pdb_00003l9y

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.258 (Depositor), 0.245 (DCC)
R-Value Work:
0.223 (Depositor), 0.214 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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This is version 1.6 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.22709
Primary Citation Related Structures:
3L9E, 3L9Y

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82205
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.258 (Depositor), 0.245 (DCC)
R-Value Work: 0.223 (Depositor), 0.214 (DCC)
R-Value Observed: 0.225 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.