3HIA | pdb_00003hia

Crystal structure of the choline binding domain of Spr1274 in Streptococcus pneumoniae

PDB DOI: https://doi.org/10.2210/pdb3HIA/pdb

Classification: CHOLINE-BINDING PROTEIN
Organism(s): Streptococcus pneumoniae R6
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-05-19 Released: 2009-08-04
Deposition Author(s): Zhang, Z.-Y., Li, W.-Z., Jiang, Y.-L., Bao, R., Zhou, C.-Z., Chen, Y.-X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.265 (Depositor), 0.273 (DCC)
R-Value Work:
0.223 (Depositor), 0.236 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of the choline-binding domain of Spr1274 in Streptococcus pneumoniae.

Zhang, Z., Li, W., Frolet, C., Bao, R., di Guilmi, A.M., Vernet, T., Chen, Y.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 757-761

PubMed: 19652332 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309109025329
Primary Citation Related Structures:
3HIA

PubMed Abstract:
Spr1274 is a putative choline-binding protein that is bound to the cell wall of Streptococcus pneumoniae through noncovalent interactions with the choline moieties of teichoic and lipoteichoic acids. Its function is still unknown. The crystal structure of the choline-binding domain of Spr1274 (residues 44-129) was solved at 2.38 A resolution with three molecules in the asymmetric unit. It may provide a structural basis for functional analysis of choline-binding proteins.

Organizational Affiliation

Protein Research Institute, Tongji University, Shanghai 200092, People's Republic of China.

Macromolecule Content

Total Structure Weight: 34.06 kDa
Atom Count: 1,973
Modeled Residue Count: 223
Deposited Residue Count: 282
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Choline binding protein	A, B, C	94	Streptococcus pneumoniae R6	Mutation(s): 0 Gene Names: spr1274
UniProt
Find proteins for Q8DP99 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DP99 Go to UniProtKB: Q8DP99
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DP99
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PC Query on PC Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] 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] H [auth B] I [auth B] D [auth A], F [auth B], G [auth B], H [auth B], I [auth B], K [auth C], L [auth C]	PHOSPHOCHOLINE C₅ H₁₅ N O₄ P YHHSONZFOIEMCP-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], M [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free: 0.265 (Depositor), 0.273 (DCC)
R-Value Work: 0.223 (Depositor), 0.236 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.61	α = 90
b = 140.61	β = 90
c = 46.05	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-08-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-08-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2025-05-07
Changes: Database references, Structure summary