8S5R

Structure of the Chlamydia pneumoniae effector SemD

• PDB DOI: https://doi.org/10.2210/pdb8S5R/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Chlamydia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-25 Released: 2024-08-07 
• Deposition Author(s): Kocher, F., Applegate, V., Reiners, J., Port, A., Spona, D., Haensch, S., Smits, S.H., Hegemann, J., Moelleken, K.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 

Starting Model: in silico

Literature

Structure of the Chlamydia pneumoniae effector SemD

Kocher, F., Applegate, V., Reiners, J., Port, A., Spona, D., Haensch, S., Smits, S.H., Hegemann, J., Moelleken, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.66 kDa 
• Atom Count: 3,776 
• Modelled Residue Count: 459 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Effector SemD	A [auth B], B [auth A]	322	Chlamydia	Mutation(s): 0  Gene Names:  CP_0070, CPn_0677, BN1224_CV15_C_01450, BN1224_GiD_A_07040, BN1224_H12_EK_00710, BN1224_MUL2216_F_02260, BN1224_Panola_J_01100, BN1224_PB1_B_06920, BN1224_U1271_C_05340, BN1224_Wien2_G_03310, BN1224_YK41_BR_01220, CWL029c_D_02120
UniProt
Find proteins for Q9Z7M7 (Chlamydia pneumoniae) Explore Q9Z7M7  Go to UniProtKB:  Q9Z7M7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.218 
• R-Value Observed: 0.221 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.999	α = 88.333
b = 51.957	β = 105.892
c = 58.628	γ = 117.433

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Kocher, F., Applegate, V., Reiners, J., Port, A., Spona, D., Haensch, S., Smits, S.H., Hegemann, J., Moelleken, K.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	417919780
German Research Foundation (DFG)	Germany	267205415

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release