4Y42 | pdb_00004y42

Cyanase (CynS) from Serratia proteamaculans

• PDB DOI: https://doi.org/10.2210/pdb4Y42/pdb

• Classification: LYASE
• Organism(s): Serratia proteamaculans 568
• Mutation(s): No 


• Deposited: 2015-02-10 Released: 2015-04-08 
• Deposition Author(s): Butryn, A., Hopfner, K.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Starting Model: experimental

Literature

Serendipitous crystallization and structure determination of cyanase (CynS) from Serratia proteamaculans

Butryn, A., Stoehr, G., Linke-Winnebeck, C., Hopfner, K.-P.

(2015) Acta Crystallogr F Struct Biol Commun 71: 471-476

• PubMed: 25849512 
• DOI: https://doi.org/10.1107/S2053230X15004902
• Primary Citation Related Structures: 
  4Y42


• PubMed Abstract: 
  

  Cyanate hydratase (CynS) catalyzes the decomposition of cyanate and bicarbonate into ammonia and carbon dioxide. Here, the serendipitous crystallization of CynS from Serratia proteamaculans (SpCynS) is reported. SpCynS was crystallized as an impurity and its identity was determined using mass-spectrometric analysis. The crystals belonged to space group P1 and diffracted to 2.1 Å resolution. The overall structure of SpCynS is very similar to a previously determined structure of CynS from Escherichia coli. Density for a ligand bound to the SpCynS active site was observed, but could not be unambiguously identified. Additionally, glycerol molecules bound at the entry to the active site of the enzyme indicate conserved residues that might be important for the trafficking of substrates and products.

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Organizational Affiliation: 
• Gene Center and Department of Biochemistry, Ludwig-Maximilians-University Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content 

• Total Structure Weight: 172.1 kDa 
• Atom Count: 13,413 
• Modeled Residue Count: 1,550 
• Deposited Residue Count: 1,560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanate hydratase	A, B, C, D, E, F, G, H, I, J	156	Serratia proteamaculans 568	Mutation(s): 0  EC: 4.2.1.104
UniProt
Find proteins for A8GBZ7 (Serratia proteamaculans (strain 568)) Explore A8GBZ7  Go to UniProtKB:  A8GBZ7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	K [auth B], L [auth G], M [auth I], N [auth J]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.200 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.549	α = 98.56
b = 82.456	β = 117.38
c = 87.985	γ = 110.46

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Butryn, A., Hopfner, K.-P.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2015-04-22
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description