3OPU

Crystal structure of the C-terminal domain of Streptococcus mutans surface protein SpaP

PDB DOI: https://doi.org/10.2210/pdb3OPU/pdb

Classification: CELL ADHESION
Organism(s): Streptococcus mutans
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-09-02 Released: 2011-01-19
Deposition Author(s): Nylander, A., Persson, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.248 (Depositor), 0.240 (DCC)
R-Value Work:
0.210 (Depositor), 0.200 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Structure of the C-terminal domain of the surface antigen SpaP from the caries pathogen Streptococcus mutans.

Nylander, A., Forsgren, N., Persson, K.

(2011) Acta Crystallogr Sect F Struct Biol Cryst Commun 67: 23-26

PubMed: 21206016 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S174430911004443X
Primary Citation of Related Structures:
3OPU

PubMed Abstract:
SpaP is a 1500-residue adhesin expressed on the surface of the caries-implicated bacterium Streptococcus mutans. SpaP is a member of the antigen I/II (AgI/II) family of proteins expressed by oral streptococci. These surface proteins are crucial for the incorporation of streptococci into dental plaque. The structure of the C-terminal domain of SpaP (residues 1136-1489) was solved and refined to 2.2 Å resolution with six molecules in the asymmetric unit. Similar to a related AgI/II structure, SpaP is stabilized by isopeptide bonds between lysine and asparagine side chains.

Organizational Affiliation

Department of Odontology, Umeå University, SE-901 87 Umeå, Sweden.

Macromolecule Content

Total Structure Weight: 228.43 kDa
Atom Count: 16,587
Modelled Residue Count: 2,029
Deposited Residue Count: 2,034
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SpaP	A, B, C, D, E A, B, C, D, E, F	339	Streptococcus mutans	Mutation(s): 0 Gene Names: SpaP
UniProt
Find proteins for P11657 (Streptococcus mutans) Explore P11657 Go to UniProtKB: P11657
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P11657
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth E] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth E] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth F]	G [auth A] H [auth A] I [auth B] J [auth B] K [auth C] G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D], O [auth E], P [auth E], Q [auth F], R [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth E] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.248 (Depositor), 0.240 (DCC)
R-Value Work: 0.210 (Depositor), 0.200 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.775	α = 90
b = 238.391	β = 90
c = 78.493	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-01-19

Deposition Author(s):

Nylander, A.

Persson, K.

Revision History (Full details and data files)

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-03-07
Changes: Data collection
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-16
Changes: Structure summary