8WG6 | pdb_00008wg6

Crystal structure of major pilin PilB from Streptococcus sanguinis - SeMet derivative

PDB DOI: https://doi.org/10.2210/pdb8WG6/pdb

Classification: CELL ADHESION
Organism(s): Streptococcus sanguinis SK36
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-20 Released: 2025-03-26
Deposition Author(s): Yadav, S., Parijat, P., Krishnan, V.
Funding Organization(s): Science and Engineering Research Board (SERB)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.269 (Depositor), 0.280 (DCC)
R-Value Work:
0.226 (Depositor), 0.238 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8WG6

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of major pilin PilB from Streptococcus sanguinis - SeMet derivative

Yadav, S., Parijat, P., Krishnan, V.

To be published.

Macromolecule Content

Total Structure Weight: 49.15 kDa
Atom Count: 3,335
Modeled Residue Count: 419
Deposited Residue Count: 451
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FimA fimbrial subunit-like protein, putative	A	451	Streptococcus sanguinis SK36	Mutation(s): 0 Gene Names: SSA_1633
UniProt
Find proteins for A3CPB6 (Streptococcus sanguinis (strain SK36)) Explore A3CPB6 Go to UniProtKB: A3CPB6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3CPB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

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: 2.40 Å
R-Value Free: 0.269 (Depositor), 0.280 (DCC)
R-Value Work: 0.226 (Depositor), 0.238 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.78	α = 90
b = 58.772	β = 90
c = 214.108	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
CRANK2	phasing
Coot	model building
REFMAC	refinement
autoPROC	data reduction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Science and Engineering Research Board (SERB)	India	CRG/2019/000432

Revision History (Full details and data files)

Version 1.0: 2025-03-26
Type: Initial release

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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.