3EPR | pdb_00003epr

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 (Depositor), 0.206 (DCC)
R-Value Work:
0.179 (Depositor), 0.176 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3EPR

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E044
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.209 (Depositor), 0.206 (DCC)
R-Value Work: 0.179 (Depositor), 0.176 (DCC)
R-Value Observed: 0.180 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2008-11-04

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.