5I69 | pdb_00005i69

MBP-MamC magnetite-interaction component mutant-D70A

• PDB DOI: https://doi.org/10.2210/pdb5I69/pdb

• Classification: Magnetite binding protein
• Organism(s): Escherichia coli, Paramagnetospirillum magneticum AMB-1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-02-16 Released: 2016-03-23 
• Deposition Author(s): Nudelman, H., Tercedor, C.V., Kolusheva, S., Gonzalez, T.P., Widdrat, M., Grimberg, N., Levi, H., Nelkenbaum, O., Davidove, G., Faivre, D., Jimenez-Lopez, C., Zarivach, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.293 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structure-function studies of the magnetite-biomineralizing magnetosome-associated protein MamC.

Nudelman, H., Valverde-Tercedor, C., Kolusheva, S., Perez Gonzalez, T., Widdrat, M., Grimberg, N., Levi, H., Nelkenbaum, O., Davidov, G., Faivre, D., Jimenez-Lopez, C., Zarivach, R.

(2016) J Struct Biol 194: 244-252

• PubMed: 26970040 
• DOI: https://doi.org/10.1016/j.jsb.2016.03.001
• Primary Citation Related Structures: 
  5I69


• PubMed Abstract: 
  

  Magnetotactic bacteria are Gram-negative bacteria that navigate along geomagnetic fields using the magnetosome, an organelle that consists of a membrane-enveloped magnetic nanoparticle. Magnetite formation and its properties are controlled by a specific set of proteins. MamC is a small magnetosome-membrane protein that is known to be active in iron biomineralization but its mechanism has yet to be clarified. Here, we studied the relationship between the MamC magnetite-interaction loop (MIL) structure and its magnetite interaction using an inert biomineralization protein-MamC chimera. Our determined structure shows an alpha-helical fold for MamC-MIL with highly charged surfaces. Additionally, the MamC-MIL induces the formation of larger magnetite crystals compared to protein-free and inert biomineralization protein control experiments. We suggest that the connection between the MamC-MIL structure and the protein's charged surfaces is crucial for magnetite binding and thus for the size control of the magnetite nanoparticles.

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Organizational Affiliation: 
• Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel.
Universidad de Granada, Departamento de Microbiologia, Campus de Fuentenueva, 18071 Granada, Spain; Department of Biomaterials, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel.
Universidad de Granada, Departamento de Microbiologia, Campus de Fuentenueva, 18071 Granada, Spain.
Universidad de Granada, Departamento de Microbiologia, Campus de Fuentenueva, 18071 Granada, Spain. Electronic address: [e-mail].
Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva, Israel. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 45.59 kDa 
• Atom Count: 3,068 
• Modeled Residue Count: 380 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Tightly bound bacterial magnetic particle protein,Maltose-binding periplasmic protein	A	412	Escherichia coli, Paramagnetospirillum magneticum AMB-1	Mutation(s): 1  Gene Names: malE, b4034, JW3994, mms13, amb0951
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
Find proteins for Q2W8S0 (Paramagnetospirillum magneticum (strain ATCC 700264 / AMB-1)) Explore Q2W8S0  Go to UniProtKB:  Q2W8S0
UniProt Groups	Q2W8S0P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	B	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.293 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.236	α = 90
b = 67.236	β = 90
c = 209.019	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Nudelman, H., Tercedor, C.V., Kolusheva, S., Gonzalez, T.P., Widdrat, M., Grimberg, N., Levi, H., Nelkenbaum, O., Davidove, G., Faivre, D., Jimenez-Lopez, C., Zarivach, R.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2016-05-04
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary