3LUP | pdb_00003lup

Crystal structure of fatty acid binding DegV family protein SAG1342 from Streptococcus agalactiae

• PDB DOI: https://doi.org/10.2210/pdb3LUP/pdb

• Classification: structure genomics, unknown function
• Organism(s): Streptococcus agalactiae 2603V/R
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-18 Released: 2010-03-02 
• Deposition Author(s): Chang, C., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal structure of fatty acid binding DegV family protein SAG1342 from Streptococcus agalactiae

Chang, C., Wu, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 31.97 kDa 
• Atom Count: 2,233 
• Modeled Residue Count: 283 
• Deposited Residue Count: 285 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DegV family protein	A	285	Streptococcus agalactiae 2603V/R	Mutation(s): 0  Gene Names: SAG1342
UniProt
Find proteins for D4AEP8 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore D4AEP8  Go to UniProtKB:  D4AEP8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ELA	B [auth A]	Elaidic acid C18 H34 O2 ZQPPMHVWECSIRJ-MDZDMXLPSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 2.65 Å
• R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.321	α = 90
b = 84.205	β = 90
c = 87.541	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
CNS	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Chang, C., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2012-02-22
  Changes: Structure summary
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.6: 2025-07-23
  Changes: Derived calculations, Structure summary