2HFB | pdb_00002hfb

Crystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb2HFB/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-06-23 Released: 2007-06-05
Deposition Author(s): Paterson, N.G., Riboldi-Tunnicliffe, A., Mitchell, T.J., Isaacs, N.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.290 (Depositor), 0.285 (DCC)
R-Value Work:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2HFB

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of selenomethionine-labelled RafE from Streptococcus pneumoniae

Paterson, N.G., Riboldi-Tunnicliffe, A., Mitchell, T.J., Isaacs, N.W.

To be published.

Macromolecule Content

Total Structure Weight: 92.75 kDa
Atom Count: 6,045
Modeled Residue Count: 764
Deposited Residue Count: 818
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, sugar-binding protein	A, B	409	Streptococcus pneumoniae TIGR4	Mutation(s): 11 Gene Names: rafE
UniProt
Find proteins for A0A0H2URJ7 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URJ7 Go to UniProtKB: A0A0H2URJ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2URJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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: 2.90 Å
R-Value Free: 0.290 (Depositor), 0.285 (DCC)
R-Value Work: 0.248 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.538	α = 90
b = 144.538	β = 90
c = 224.082	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Riboldi-Tunnicliffe, A.

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2008-04-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-10-30
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.