4HP5 | pdb_00004hp5

The crystal structure of isomaltulose synthase mutant E295A from Erwinia rhapontici NX5 in complex with D-glucose

• PDB DOI: https://doi.org/10.2210/pdb4HP5/pdb

• Classification: ISOMERASE
• Organism(s): Erwinia rhapontici
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-10-23 Released: 2013-11-13 
• Deposition Author(s): Xu, Z., Li, S., Xu, H., Zhou, J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of isomaltulose synthase mutant E295A from Erwinia rhapontici NX5 in complex with D-glucose

Xu, Z., Li, S., Xu, H., Zhou, J.

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)

Macromolecule Content 

• Total Structure Weight: 66.09 kDa 
• Atom Count: 5,251 
• Modeled Residue Count: 559 
• Deposited Residue Count: 559 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose isomerase	A	559	Erwinia rhapontici	Mutation(s): 1  Gene Names: PalI EC: 5.4.99.11
UniProt
Find proteins for D9MPF2 (Erwinia rhapontici) Explore D9MPF2  Go to UniProtKB:  D9MPF2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLC	D [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.849	α = 90
b = 81.325	β = 90
c = 138.258	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-13 
Deposition Author(s): Xu, Z., Li, S., Xu, H., Zhou, J.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary