6R41

Structure of P110 from Mycoplasma genitalium complexed with 3'SL

• PDB DOI: https://doi.org/10.2210/pdb6R41/pdb
• Entry: 6R41 supersedes: 5MZ9

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mycoplasmoides genitalium G37
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-03-21 Released: 2019-05-08 
• Deposition Author(s): Aparicio, D., Fita, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 100.43 kDa 
• Atom Count: 7,124 
• Modelled Residue Count: 886 
• Deposited Residue Count: 916 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mgp-operon protein 3	A	916	Mycoplasmoides genitalium G37	Mutation(s): 0  Gene Names: MG192
UniProt
Find proteins for P22747 (Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37)) Explore P22747  Go to UniProtKB:  P22747

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G30207PZ GlyCosmos:  G30207PZ GlyGen:  G30207PZ

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	D [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
K	C [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.216 
• R-Value Work: 0.190 
• R-Value Observed: 0.191 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.026	α = 90
b = 151.569	β = 90
c = 176.548	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): Aparicio, D., Fita, I.
• This entry supersedes: 5MZ9

Revision History  

• Version 1.0: 2019-05-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary
• Version 2.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary