4F2D | pdb_00004f2d

Crystal Structure of Escherichia coli L-arabinose Isomerase (ECAI) complexed with Ribitol

• PDB DOI: https://doi.org/10.2210/pdb4F2D/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-05-07 Released: 2012-05-30 
• Deposition Author(s): Manjasetty, B.A., Burley, S.K., Almo, S.C., Chance, M.R., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Escherichia coli L-arabinose Isomerase (ECAI) complexed with Ribitol

Manjasetty, B.A., Burley, S.K., Almo, S.C., Chance, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 171.58 kDa 
• Atom Count: 11,787 
• Modeled Residue Count: 1,494 
• Deposited Residue Count: 1,500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-arabinose isomerase	A, B, C	500	Escherichia coli K-12	Mutation(s): 0  Gene Names: araA, b0062, JW0061, UTI89_C0067 EC: 5.3.1.4
UniProt
Find proteins for P08202 (Escherichia coli (strain K12)) Explore P08202  Go to UniProtKB:  P08202

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RB0	E [auth A], G [auth B], J [auth C]	D-ribitol C5 H12 O5 HEBKCHPVOIAQTA-ZXFHETKHSA-N
ACY	H [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MN	D [auth A], F [auth B], I [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.472	α = 90
b = 116.472	β = 90
c = 214.81	γ = 120

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Manjasetty, B.A., Burley, S.K., Almo, S.C., Chance, M.R., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary