3BED | pdb_00003bed

Mannose/sorbose specific IIA subunit of phosphotransferase system from Enterococcus faecalis

PDB DOI: https://doi.org/10.2210/pdb3BED/pdb
Entry: 3BED supersedes: 2IAC

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-11-16 Released: 2007-11-27
Deposition Author(s): Osipiuk, J., Wu, R., Moy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.197 (Depositor), 0.194 (DCC)
R-Value Work:
0.157 (Depositor), 0.156 (DCC)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BED

This is version 1.2 of the entry. See complete history.

Literature

X-Ray Crystal Structure of Mannose/sorbose specific IIa subunit of phosphotransferase system from Enterococcus faecalis.

Osipiuk, J., Wu, R., Moy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 30.61 kDa
Atom Count: 2,355
Modeled Residue Count: 261
Deposited Residue Count: 284
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system, IIA component	A, B	142	Enterococcus faecalis V583	Mutation(s): 0 Gene Names: EF_0461
UniProt
Find proteins for Q838I6 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q838I6 Go to UniProtKB: Q838I6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q838I6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY Query on MLY	A, B	L-PEPTIDE LINKING	C₈ H₁₈ N₂ O₂		LYS
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.197 (Depositor), 0.194 (DCC)
R-Value Work: 0.157 (Depositor), 0.156 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.059	α = 90
b = 37.503	β = 121.49
c = 76.993	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-11-27

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

This entry supersedes: 2IAC

Revision History (Full details and data files)

Version 1.0: 2007-11-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary

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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.