5T0W | pdb_00005t0w

Crystal structure of the ancestral amino acid-binding protein AncCDT-1, a precursor of cyclohexadienyl dehydratase

• PDB DOI: https://doi.org/10.2210/pdb5T0W/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-16 Released: 2017-09-06 
• Deposition Author(s): Clifton, B.E., Carr, P.D., Jackson, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.255 (Depositor) 

Starting Model: experimental

Literature

To be published

Clifton, B.E., Kaczmarski, J.A., Carr, P.D., Jackson, C.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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

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

Biological Assembly Evidence: gel filtration

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 111.82 kDa 
• Atom Count: 7,011 
• Modeled Residue Count: 910 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AncCDT-1	A, B, C, D	247	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ARG	E [auth A], F [auth B], G [auth C], H [auth D]	ARGININE C6 H15 N4 O2 ODKSFYDXXFIFQN-BYPYZUCNSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.253 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.255 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.03	α = 90
b = 68.88	β = 90
c = 318.63	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-06 
Deposition Author(s): Clifton, B.E., Carr, P.D., Jackson, C.J.

Revision History  

• Version 1.0: 2017-09-06
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description