9OW2 | pdb_00009ow2

Crystal Structure of the Surface Protein (CD630_07380) from Clostridium difficile Strain 630

PDB DOI: https://doi.org/10.2210/pdb9OW2/pdb

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

Deposited: 2025-06-02 Released: 2025-06-18
Deposition Author(s): Minasov, G., Shuvalova, L., Kiryukhina, O., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 ?
R-Value Free:
0.224 (Depositor), 0.234 (DCC)
R-Value Work:
0.179 (Depositor), 0.192 (DCC)
R-Value Observed:
0.181 (Depositor)

Starting Model: in silico
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of the Surface Protein (CD630_07380) from Clostridium difficile Strain 630.

Minasov, G., Shuvalova, L., Kiryukhina, O., Satchell, K.J.F., Center for Structural Biology of Infectious Diseases (CSBID)

To be published.

Macromolecule Content

Total Structure Weight: 66.93 kDa
Atom Count: 4,541
Modeled Residue Count: 509
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exported protein	A, B	275	Clostridioides difficile 630	Mutation(s): 0 Gene Names: CD630_07380
UniProt
Find proteins for Q189T6 (Clostridioides difficile (strain 630)) Explore Q189T6 Go to UniProtKB: Q189T6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q189T6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PE3 Query on PE3 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL C₂₈ H₅₈ O₁₅ ILLKMACMBHTSHP-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B]	O [auth B], P [auth B], Q [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME Query on CME	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 ?
R-Value Free: 0.224 (Depositor), 0.234 (DCC)
R-Value Work: 0.179 (Depositor), 0.192 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 42.08	α = 90
b = 94.872	β = 89.99
c = 57.093	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Center for Structural Biology of Infectious Diseases (CSBID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	75N93022C00035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C