1YCO | pdb_00001yco

Crystal structure of a branched-chain phosphotransacylase from Enterococcus faecalis V583

• PDB DOI: https://doi.org/10.2210/pdb1YCO/pdb

• Classification: TRANSFERASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-12-22 Released: 2005-01-18 
• Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a branched-chain phosphotransacylase from Enterococcus faecalis V583

Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D.

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: 61.11 kDa 
• Atom Count: 4,314 
• Modeled Residue Count: 543 
• Deposited Residue Count: 558 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
branched-chain phosphotransacylase	A, B	279	Enterococcus faecalis V583	Mutation(s): 0  Gene Names: ptb
UniProt
Find proteins for Q834I9 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q834I9  Go to UniProtKB:  Q834I9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.283 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.165	α = 90
b = 61.165	β = 90
c = 317.995	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Rajashankar, K.R., Kniewel, R., Lee, K., Lima, C.D., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references
• Version 1.5: 2024-04-03
  Changes: Refinement description