5E7U | pdb_00005e7u

MBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1

• PDB DOI: https://doi.org/10.2210/pdb5E7U/pdb

• Classification: Magnetite binding protein
• Organism(s): Escherichia coli, Paramagnetospirillum magneticum AMB-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-10-13 Released: 2016-03-23 
• Deposition Author(s): Nudelman, H., Zarivach, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.307 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Observed: 
  0.270 (Depositor) 

Starting Model: experimental

Literature

MBP-MamC loop structure, a magnetite biomineralizing protein from Magnetospirillium magneticum AMB-1

Nudelman, H., Zarivach, R.

To be published.

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: 45.82 kDa 
• Atom Count: 3,006 
• 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): 0  Gene Names: malE, Z5632, ECs5017, mms13, amb0951
UniProt
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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], D [auth A], E [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: 2.80 Å
• R-Value Free:  0.307 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Observed: 0.270 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.6	α = 90
b = 66.6	β = 90
c = 211.137	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Nudelman, H., Zarivach, R.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• 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