7K1U

Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630

PDB DOI: https://doi.org/10.2210/pdb7K1U/pdb

Classification: CELL ADHESION
Organism(s): Clostridioides difficile 630
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-09-08 Released: 2021-10-20
Deposition Author(s): Minasov, G., Shuvalova, L., Rosas-Lemus, M., Wiersum, G., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.217
R-Value Work: 0.174
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of SrtB-anchored Collagen-binding Adhesin Fragment (residues 206-565) from Clostridioides difficile strain 630

Minasov, G., Shuvalova, L., Rosas-Lemus, M., Wiersum, G., Satchell, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 39.66 kDa
Atom Count: 2,115
Modelled Residue Count: 253
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen-binding Adhesin	A	365	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_03860
UniProt
Find proteins for Q18DC3 (Clostridioides difficile (strain 630)) Explore Q18DC3 Go to UniProtKB: Q18DC3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q18DC3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTB Query on BTB 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]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₈ H₁₉ N O₅ OWMVSZAMULFTJU-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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: 0.217
R-Value Work: 0.174
R-Value Observed: 0.176
Space Group: P 3₁ 2 1
Diffraction Data: https://doi.org/10.18430/m37k1u

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.323	α = 90
b = 69.323	β = 90
c = 187.527	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2021-10-20

Deposition Author(s):

Rosas-Lemus, M.

Satchell, K.J.F.

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2021-10-20
Type: Initial release
Version 1.1: 2021-11-10
Changes: Database references
Version 1.2: 2024-10-09
Changes: Data collection, Structure summary

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.