4H8U | pdb_00004h8u

MUTB inactive double mutant D200A-D415N soaked with sucrose and having as bound ligands sucrose in molecule A and the reaction product trehalulose in molecule B

• PDB DOI: https://doi.org/10.2210/pdb4H8U/pdb

• Classification: ISOMERASE
• Organism(s): Rhizobium sp. MX-45
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-09-24 Released: 2013-09-25 
• Deposition Author(s): Lipski, A., Haser, R., Aghajari, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Insights into product binding in sucrose isomerases from crystal structures of MutB from Rhizobium sp.

Lipski, A., Watzlawick, H., Ravaud, S., Robert, X., Haser, R., Mattes, R., Aghajari, N.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 128.64 kDa 
• Atom Count: 10,522 
• Modeled Residue Count: 1,108 
• Deposited Residue Count: 1,114 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose isomerase	A, B	557	Rhizobium sp. MX-45	Mutation(s): 2  Gene Names: mutB
UniProt
Find proteins for M1E1F6 (Rhizobium sp. MX-45) Explore M1E1F6  Go to UniProtKB:  M1E1F6

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TEU	F [auth B]	1-O-alpha-D-glucopyranosyl-D-fructose C12 H22 O11 NMELTECMHKKXLF-DGQJZECASA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.37	α = 66.15
b = 73.68	β = 74.29
c = 82.67	γ = 72.42

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-25 
Deposition Author(s): Lipski, A., Haser, R., Aghajari, N.

Revision History  

• Version 1.0: 2013-09-25
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary