6I1H | pdb_00006i1h

Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with meropenem

• PDB DOI: https://doi.org/10.2210/pdb6I1H/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Chlamydia trachomatis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-10-28 Released: 2019-11-20 
• Deposition Author(s): Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with meropenem

Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.71 kDa 
• Atom Count: 5,241 
• Modeled Residue Count: 676 
• Deposited Residue Count: 692 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein,Penicillin-binding protein	A, B	346	Chlamydia trachomatis	Mutation(s): 0  Gene Names: pbp_2, ERS133248_00492 EC: 2.4.1.129

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MER (Subject of Investigation/LOI)	C [auth A], D [auth B]	(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid C17 H27 N3 O5 S DYQHXZPAIVAJRU-HTXLXMOSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.251 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.566	α = 90
b = 112.566	β = 90
c = 118.501	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
MrBUMP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-11-20 
Deposition Author(s): Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	grant.MR/P007503/1

Revision History  

• Version 1.0: 2019-11-20
  Type: Initial release
  
• Version 1.1: 2020-07-08
  Changes: Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description