5KKW | pdb_00005kkw

Crystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-methylpiperidinium-1-yl)propane-1-sulfonate)

• PDB DOI: https://doi.org/10.2210/pdb5KKW/pdb
• Entry: 5KKW supersedes: 5HMT

• Classification: LYASE
• Organism(s): Candidatus Pelagibacter ubique HTCC1062
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-06-22 Released: 2017-07-05 
• Deposition Author(s): Clifton, B.E., Carr, P.D., Jackson, C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of SAR11_1068 bound to a sulfobetaine (3-(1-methylpiperidinium-1-yl)propane-1-sulfonate)

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

Macromolecule Content 

• Total Structure Weight: 28.22 kDa 
• Atom Count: 1,972 
• Modeled Residue Count: 237 
• Deposited Residue Count: 249 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclohexadienyl dehydratase	A	249	Candidatus Pelagibacter ubique HTCC1062	Mutation(s): 0  Gene Names: pheC, SAR11_1068
UniProt
Find proteins for Q4FLR5 (Pelagibacter ubique (strain HTCC1062)) Explore Q4FLR5  Go to UniProtKB:  Q4FLR5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KH2	B [auth A]	3-(1-methylpiperidinium-1-yl)propane-1-sulfonate C9 H19 N O3 S DQNQWAVIDNVATL-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.665	α = 90
b = 77.665	β = 90
c = 44.851	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-07-05 
Deposition Author(s): Clifton, B.E., Carr, P.D., Jackson, C.J.
• This entry supersedes: 5HMT

Revision History  

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Author supporting evidence
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Refinement description