3FNA | pdb_00003fna

Crystal structure of the CBS pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073

• PDB DOI: https://doi.org/10.2210/pdb3FNA/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli CFT073
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-12-23 Released: 2009-01-27 
• Deposition Author(s): Cuff, M.E., Bigelow, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.243 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.257 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

The CBS Pair of possible D-arabinose 5-phosphate isomerase yrbH from Escherichia coli CFT073

Cuff, M.E., Bigelow, L., Buck, K., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.2 kDa 
• Atom Count: 2,053 
• Modeled Residue Count: 243 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible arabinose 5-phosphate isomerase	A, B	149	Escherichia coli CFT073	Mutation(s): 0  Gene Names: c3957

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], D [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.243 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.257 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.109	α = 90
b = 108.458	β = 90
c = 104.849	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Cuff, M.E., Bigelow, L., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary