7LSR

Ruminococcus bromii Amy12-D392A with maltoheptaose

• PDB DOI: https://doi.org/10.2210/pdb7LSR/pdb

• Classification: HYDROLASE
• Organism(s): Ruminococcus bromii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-02-18 Released: 2021-07-14 
• Deposition Author(s): Koropatkin, N.M., Cockburn, D.W., Brown, H.A., Kibler, R.D.
• Funding Organization(s): United States - Israel Binational Science Foundation (BSF)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.228 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

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: 88.96 kDa 
• Atom Count: 6,280 
• Modelled Residue Count: 761 
• Deposited Residue Count: 797 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pullulanase	A	797	Ruminococcus bromii	Mutation(s): 1  Gene Names: pulA_2, RBL236_00821 EC: 3.2.1.41
UniProt
Find proteins for A0A2N0UU23 (Ruminococcus bromii) Explore A0A2N0UU23  Go to UniProtKB:  A0A2N0UU23

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	5		N/A
Glycosylation Resources
GlyTouCan:  G43441FW GlyCosmos:  G43441FW

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan:  G96370VA GlyCosmos:  G96370VA GlyGen:  G96370VA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009	C	alpha-maltotriose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.228 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.029	α = 90
b = 98.231	β = 90
c = 170.279	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Koropatkin, N.M., Cockburn, D.W., Brown, H.A., Kibler, R.D.

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Funding Organization	Location	Grant Number
United States - Israel Binational Science Foundation (BSF)	United States	--

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description