3FCD | pdb_00003fcd

Crystal Structure of a putative glyoxalase from an environmental bacteria

• PDB DOI: https://doi.org/10.2210/pdb3FCD/pdb

• Classification: LYASE
• Organism(s): uncultured bacterium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-21 Released: 2008-12-09 
• Deposition Author(s): Silberstein, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 
  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.229 (DCC) 

Literature

Crystal Structure of a putative glyoxalase from an environmental bacteria

Silberstein, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 30.89 kDa 
• Atom Count: 2,064 
• Modeled Residue Count: 236 
• Deposited Residue Count: 268 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lyase	A, B	134	uncultured bacterium	Mutation(s): 0
UniProt
Find proteins for A0ACD6B844 (uncultured bacterium) Explore A0ACD6B844  Go to UniProtKB:  A0ACD6B844

Small Molecules

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: 1.92 Å
• R-Value Free:  0.276 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.229 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.63	α = 90
b = 37.277	β = 98.7
c = 72.117	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Silberstein, M., Eswaramoorthy, S., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-12-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references
• Version 1.4: 2024-11-06
  Changes: Structure summary