3EPR

Crystal structure of putative HAD superfamily hydrolase from Streptococcus agalactiae.

• PDB DOI: https://doi.org/10.2210/pdb3EPR/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus agalactiae serogroup V
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-29 Released: 2008-11-04 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Dickey, M., Tang, B.K., Groshong, C., Rodgers, L., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Crystal structure of putative HAD superfamily hydrolase from Streptococcus agalactiae.

Ramagopal, U.A., Toro, R., Dickey, M., Tang, B.K., Groshong, C., Rodgers, L., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.23 kDa 
• Atom Count: 2,297 
• Modelled Residue Count: 260 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hydrolase, haloacid dehalogenase-like family	A	264	Streptococcus agalactiae serogroup V	Mutation(s): 0  Gene Names: SAG0892 EC: 3.1.3
UniProt
Find proteins for Q8E044 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8E044  Go to UniProtKB:  Q8E044

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 0.209 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.367	α = 90
b = 82.954	β = 90
c = 99.604	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
SHELXE	model building
SHELXD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-04 
Deposition Author(s): Ramagopal, U.A., Toro, R., Dickey, M., Tang, B.K., Groshong, C., Rodgers, L., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2008-11-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references