2HEU | pdb_00002heu

Atomic resolution structure of apo-form of RafE from Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb2HEU/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-06-22 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: 1.04 Å
R-Value Free:
0.157 (Depositor), 0.165 (DCC)
R-Value Work:
0.130 (Depositor), 0.139 (DCC)
R-Value Observed:
0.131 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 2HEU

This is version 1.5 of the entry. See complete history.

Literature

High resolution crystal structures of RafE from Streptococcus pneumoniae.

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

To be published.

Macromolecule Content

Total Structure Weight: 135.69 kDa
Atom Count: 12,875
Modeled Residue Count: 1,171
Deposited Residue Count: 1,203
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter, sugar-binding protein	A, B, C	401	Streptococcus pneumoniae	Mutation(s): 0 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain E [auth A] MOL2 format, chain H [auth C] MOL2 format, chain E [auth A] mmCIF format, chain H [auth C] mmCIF format, chain E [auth A]	E [auth A], H [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.04 Å
R-Value Free: 0.157 (Depositor), 0.165 (DCC)
R-Value Work: 0.130 (Depositor), 0.139 (DCC)
R-Value Observed: 0.131 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.219	α = 90
b = 129.315	β = 94.21
c = 119.42	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection

Structure Validation

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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: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2022-12-21
Changes: Database references, Derived calculations
Version 1.5: 2024-05-29
Changes: Data collection

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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.