8ZYG

Crystal structure of a cupin protein (tm1459, I49C-4py/H52A/C106D mutant) in copper (Cu) substituted form

• PDB DOI: https://doi.org/10.2210/pdb8ZYG/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-06-17 Released: 2024-09-04 
• Deposition Author(s): Morita, Y., Kubo, H., Matsumoto, R., Fujieda, N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.171 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Starting Model: experimental

Literature

Copper center in artificial non-heme metalloenzyme

Morita, Y., Kubo, H., Matsumoto, R., Fujieda, N.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 27.39 kDa 
• Atom Count: 2,185 
• Modelled Residue Count: 233 
• Deposited Residue Count: 236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cupin type-2 domain-containing protein	A, B	118	Thermotoga maritima MSB8	Mutation(s): 3  Gene Names: TM_1459
UniProt
Find proteins for Q9X1H0 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1H0  Go to UniProtKB:  Q9X1H0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	C [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
MES	E [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
CU	D [auth A], F [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS	A, B	L-PEPTIDE LINKING	C3 H7 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 0.171 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.67	α = 90
b = 57.57	β = 90
c = 75.87	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-04 
Deposition Author(s): Morita, Y., Kubo, H., Matsumoto, R., Fujieda, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21KK0249
Japan Society for the Promotion of Science (JSPS)	Japan	23K13764
Japan Society for the Promotion of Science (JSPS)	Japan	JP21H01954
Japan Society for the Promotion of Science (JSPS)	Japan	24K01503

Revision History  

• Version 1.0: 2024-09-04
  Type: Initial release