3RUM

New strategy to analyze structures of glycopeptide antibiotic-target complexes

• PDB DOI: https://doi.org/10.2210/pdb3RUM/pdb

• Classification: SUGAR BINDING PROTEIN/ANTIBIOTIC
• Organism(s): Escherichia coli K-12, Amycolatopsis lurida
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-05-05 Released: 2012-06-06 
• Deposition Author(s): Economou, N.J., Weeks, S.D., Grasty, K.C., Nahoum, V., Loll, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.219 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.51 kDa 
• Atom Count: 3,645 
• Modelled Residue Count: 392 
• Deposited Residue Count: 392 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein	A	378	Escherichia coli K-12	Mutation(s): 0  Gene Names: malE, b4034, JW3994
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ristocetin	B, C	7	Amycolatopsis lurida	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-arabinofuranose-(1-2)-alpha-D-mannopyranose-(1-2)-[alpha-L-rhamnopyranose-(1-6)]beta-D-glucopyranose	D, E	4		N/A
Glycosylation Resources
GlyTouCan:  G77120YG GlyCosmos:  G77120YG

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN	N [auth B], P [auth C]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
RST	M [auth B], O [auth C]	3-amino-2,3,6-trideoxy-alpha-L-ribo-hexopyranose C6 H13 N O3 BBMKQGIZNKEDOX-KCDKBNATSA-N
SO4	J [auth A], K [auth A], L [auth A], Q [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
IPA	G [auth A], H [auth A], I [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Modified Residues  3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CCS	A	L-PEPTIDE LINKING	C5 H9 N O4 S		CYS
MDF	B, C	L-PEPTIDE LINKING	C9 H11 N O4		TYR
OMX	B, C	L-PEPTIDE LINKING	C9 H11 N O4		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	F	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.219 
• R-Value Work: 0.176 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.833	α = 90
b = 75.005	β = 90
c = 90.778	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Economou, N.J., Weeks, S.D., Grasty, K.C., Nahoum, V., Loll, P.J.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2016-02-17
  Changes: Derived calculations, Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary
• Version 2.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-12-06
  Changes: Data collection, Derived calculations