3FBG | pdb_00003fbg

Crystal structure of a putative arginate lyase from Staphylococcus haemolyticus

• PDB DOI: https://doi.org/10.2210/pdb3FBG/pdb

• Classification: structural genomics, unknown function
• Organism(s): Staphylococcus haemolyticus JCSC1435
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-11-19 Released: 2008-12-09 
• Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.275 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Literature

Crystal structure of a putative arginate lyase from Staphylococcus haemolyticus

Bonanno, J.B., Gilmore, M., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 77.75 kDa 
• Atom Count: 5,824 
• Modeled Residue Count: 668 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative arginate lyase	A, B	346	Staphylococcus haemolyticus JCSC1435	Mutation(s): 0  Gene Names: SH0852
UniProt
Find proteins for Q4L864 (Staphylococcus haemolyticus (strain JCSC1435)) Explore Q4L864  Go to UniProtKB:  Q4L864

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.275 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.198	α = 90
b = 93.552	β = 98.86
c = 83.24	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXCD	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-09 
Deposition Author(s): Bonanno, J.B., Gilmore, M., Bain, K.T., Do, J., Romero, R., Wasserman, S., Sauder, J.M., Burley, S.K., Almo, S.C., 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: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references