6ZIF | pdb_00006zif

The structure of a cytosolic copper storage protein from Methylocystis sp. Strain Rockwell (ATCC 49242)

• PDB DOI: https://doi.org/10.2210/pdb6ZIF/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Methylocystis sp. ATCC 49242
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-25 Released: 2022-01-12 
• Deposition Author(s): Basle, A., Lee, J., Dennison, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.270 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

The importance of sites at the entrance of a copper storage protein for Cu(I) binding and removal

Lee, J., Basle, A., Dennison, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 52.79 kDa 
• Atom Count: 3,316 
• Modeled Residue Count: 430 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RkCSP3	A, B, C, D	108	Methylocystis sp. ATCC 49242	Mutation(s): 0
UniProt
Find proteins for A0ACD6BAU7 (Methylocystis sp. ATCC 49242) Explore A0ACD6BAU7  Go to UniProtKB:  A0ACD6BAU7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	EB [auth C], V [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU1 (Subject of Investigation/LOI)	AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], E [auth A], EA [auth B], F [auth A], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MA [auth B], MB [auth D], N [auth A], NA [auth C], NB [auth D], O [auth A], OA [auth C], OB [auth D], P [auth A], PA [auth C], PB [auth D], Q [auth A], QA [auth C], QB [auth D], R [auth A], RA [auth C], RB [auth D], S [auth A], SA [auth C], SB [auth D], T [auth A], TA [auth C], TB [auth D], U [auth A], UA [auth C], UB [auth D], VA [auth C], VB [auth D], W [auth B], WA [auth C], X [auth B], XA [auth C], Y [auth B], YA [auth C], Z [auth B], ZA [auth C]	COPPER (I) ION Cu VMQMZMRVKUZKQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.270 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.76	α = 90
b = 60.76	β = 90
c = 231.93	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data processing
Aimless	data scaling
Coot	model building
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-01-12 
Deposition Author(s): Basle, A., Lee, J., Dennison, C.

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Refinement description