2R48 | pdb_00002r48

Crystal structure of the fructose specific IIB subunit of PTS system from Bacillus subtilis subsp. subtilis str. 168

PDB DOI: https://doi.org/10.2210/pdb2R48/pdb

Classification: TRANSFERASE, TRANSPORT PROTEIN
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-08-30 Released: 2007-09-11
Deposition Author(s): Nocek, B., Cuff, M., Sather, A., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.237 (Depositor), 0.244 (DCC)
R-Value Work:
0.183 (Depositor), 0.191 (DCC)
R-Value Observed:
0.186 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2R48

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

Literature

Crystal structure of the fructose specific IIB subunit of PTS system from Bacillus subtilis subsp. subtilis str. 168.

Nocek, B., Cuff, M., Sather, A., Clancy, S., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 11.48 kDa
Atom Count: 855
Modeled Residue Count: 105
Deposited Residue Count: 106
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotransferase system (PTS) mannose-specific enzyme IIBCA component	A	106	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: manP, BSU12010 EC: 2.7.1.191
UniProt
Find proteins for O31645 (Bacillus subtilis (strain 168)) Explore O31645 Go to UniProtKB: O31645
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O31645
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.237 (Depositor), 0.244 (DCC)
R-Value Work: 0.183 (Depositor), 0.191 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.931	α = 90
b = 48.931	β = 90
c = 68.25	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Source and taxonomy, Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.