8SMQ

Crystal Structure of the N-terminal Domain of the Cryptic Surface Protein (CD630_25440) from Clostridium difficile.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Protein target highlights in CASP15: Analysis of models by structure providers.

Alexander, L.T.Durairaj, J.Kryshtafovych, A.Abriata, L.A.Bayo, Y.Bhabha, G.Breyton, C.Caulton, S.G.Chen, J.Degroux, S.Ekiert, D.C.Erlandsen, B.S.Freddolino, P.L.Gilzer, D.Greening, C.Grimes, J.M.Grinter, R.Gurusaran, M.Hartmann, M.D.Hitchman, C.J.Keown, J.R.Kropp, A.Kursula, P.Lovering, A.L.Lemaitre, B.Lia, A.Liu, S.Logotheti, M.Lu, S.Markusson, S.Miller, M.D.Minasov, G.Niemann, H.H.Opazo, F.Phillips Jr., G.N.Davies, O.R.Rommelaere, S.Rosas-Lemus, M.Roversi, P.Satchell, K.Smith, N.Wilson, M.A.Wu, K.L.Xia, X.Xiao, H.Zhang, W.Zhou, Z.H.Fidelis, K.Topf, M.Moult, J.Schwede, T.

(2023) Proteins 91: 1571-1599

  • DOI: https://doi.org/10.1002/prot.26545
  • Primary Citation of Related Structures:  
    8SMQ

  • PubMed Abstract: 

    We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.


  • Organizational Affiliation

    Biozentrum, University of Basel, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hypothetical protein CD630_25440
A, B, C, D
173Clostridioides difficile 630Mutation(s): 0 
Gene Names: CD630_25440
UniProt
Find proteins for Q182N1 (Clostridioides difficile (strain 630))
Explore Q182N1 
Go to UniProtKB:  Q182N1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ182N1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
O [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
I [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth D],
V [auth D],
W [auth D],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
OCS
Query on OCS
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.797α = 90
b = 81.302β = 128.81
c = 93.751γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00035
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700060C

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-15
    Changes: Data collection
  • Version 1.3: 2023-12-06
    Changes: Database references