2IPM | pdb_00002ipm

Crystal structure of a disulfide mutant glucose binding protein

• PDB DOI: https://doi.org/10.2210/pdb2IPM/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2006-10-12 Released: 2007-03-20 
• Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free: 
  0.179 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

The free energy cost of domain reorganization in E. coli glucose binding protein

Cuneo, M.J., Hellinga, H.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.71 kDa 
• Atom Count: 2,922 
• Modeled Residue Count: 307 
• Deposited Residue Count: 318 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-galactose-binding periplasmic protein	A	318	Escherichia coli	Mutation(s): 2  Gene Names: mglB
UniProt
Find proteins for P0AEE5 (Escherichia coli (strain K12)) Explore P0AEE5  Go to UniProtKB:  P0AEE5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	B [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.12 Å
• R-Value Free:  0.179 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.19	α = 90
b = 36.6	β = 106.81
c = 64.82	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Cuneo, M.J., Hellinga, H.W.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references, Structure summary
• Version 1.6: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.7: 2024-11-20
  Changes: Structure summary