6H5U | pdb_00006h5u

MamM CTD H264E - Zinc form 2

• PDB DOI: https://doi.org/10.2210/pdb6H5U/pdb

• Classification: METAL TRANSPORT
• Organism(s): Magnetospirillum gryphiswaldense
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-07-25 Released: 2019-08-07 
• Deposition Author(s): Barber-Zucker, S., Zarivach, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

MamM CTD H264E - Zinc form 2

Barber-Zucker, S., Zarivach, R.

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 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.23 kDa 
• Atom Count: 2,304 
• Modeled Residue Count: 271 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Magnetosome protein MamM, Cation efflux protein family	A, B, C, D [auth H]	108	Magnetospirillum gryphiswaldense	Mutation(s): 1  Gene Names: mamM, mgI491, MGR_4095
UniProt
Find proteins for V6F235 (Magnetospirillum gryphiswaldense (strain DSM 6361 / JCM 21280 / NBRC 15271 / MSR-1)) Explore V6F235  Go to UniProtKB:  V6F235

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BME	G [auth A], I [auth B], L [auth C]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
ZN	E [auth A], J [auth C], K [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.049	α = 90
b = 55.648	β = 92.14
c = 63.767	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Barber-Zucker, S., Zarivach, R.

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Funding Organization	Location	Grant Number
	Israel	Israel Science Foundation 167/16
	Israel	Israel Ministry of Science, Technology and Space

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description