1YIS | pdb_00001yis

Structural genomics of Caenorhabditis elegans: adenylosuccinate lyase

• PDB DOI: https://doi.org/10.2210/pdb1YIS/pdb

• Classification: LYASE
• Organism(s): Caenorhabditis elegans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-12 Released: 2005-01-25 
• Deposition Author(s): Symersky, J., Schormann, N., Lu, S., Zhang, Y., Karpova, E., Qiu, S., Huang, W., Cao, Z., Zhou, J., Luo, M., Arabshahi, A., McKinstry, A., Luan, C.-H., Luo, D., Johnson, D., An, J., Tsao, J., Delucas, L., Shang, Q., Gray, R., Li, S., Bray, T., Chen, Y.-J., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.202 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.184 (DCC) 

Literature

Structural genomics of Caenorhabditis elegans: adenylosuccinate lyase

Symersky, J., Schormann, N., Lu, S., Zhang, Y., Karpova, E., Qiu, S., Huang, W., Cao, Z., Zhou, J., Luo, M., Arabshahi, A., McKinstry, A., Luan, C.-H., Luo, D., Johnson, D., An, J., Tsao, J., Delucas, L., Shang, Q., Gray, R., Li, S., Bray, T., Chen, Y.-J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 54.3 kDa 
• Atom Count: 3,551 
• Modeled Residue Count: 421 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adenylosuccinate lyase	A	478	Caenorhabditis elegans	Mutation(s): 12  EC: 4.3.2.2
UniProt
Find proteins for Q21774 (Caenorhabditis elegans) Explore Q21774  Go to UniProtKB:  Q21774

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.202 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.184 (DCC) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.242	α = 90
b = 124.242	β = 90
c = 165.127	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
HKL-2000	data reduction
SOLVE	phasing
RESOLVE	model building
CNS	refinement
HKL-2000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-25 
Deposition Author(s): Symersky, J., Schormann, N., Lu, S., Zhang, Y., Karpova, E., Qiu, S., Huang, W., Cao, Z., Zhou, J., Luo, M., Arabshahi, A., McKinstry, A., Luan, C.-H., Luo, D., Johnson, D., An, J., Tsao, J., Delucas, L., Shang, Q., Gray, R., Li, S., Bray, T., Chen, Y.-J., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2005-01-25
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary