7Z7Y | pdb_00007z7y

REP-related Chom18 variant with double GT mismatch

• PDB DOI: https://doi.org/10.2210/pdb7Z7Y/pdb
• NAKB: 7Z7Y

• Classification: DNA
• Organism(s): Cardiobacterium hominis
• Mutation(s): No 


• Deposited: 2022-03-16 Released: 2023-03-29 
• Deposition Author(s): Svoboda, J., Schneider, B., Berdar, D., Kolenko, P.
• Funding Organization(s): Ministry of Education, Youth and Sports of the Czech Republic, Czech Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.319 (Depositor), 0.318 (DCC) 
• R-Value Work: 
  0.258 (Depositor), 0.269 (DCC) 
• R-Value Observed: 
  0.272 (Depositor) 

Starting Model: experimental

Literature

Conformation-based refinement of 18-mer DNA structures.

Svoboda, J., Berdar, D., Kolenko, P., Cerny, J., Novakova, Z., Pavlicek, J., Schneider, B.

(2023) Acta Crystallogr D Struct Biol 79: 655-665

• PubMed: 37338420 
• DOI: https://doi.org/10.1107/S2059798323004679
• Primary Citation Related Structures: 
  7Z7K, 7Z7L, 7Z7M, 7Z7U, 7Z7W, 7Z7Y, 7Z7Z, 7Z81, 7Z82


• PubMed Abstract: 
  

  Nine new crystal structures of CG-rich DNA 18-mers with the sequence 5'-GGTGGGGGC-XZ-GCCCCACC-3', which are related to the bacterial repetitive extragenic palindromes, are reported. 18-mer oligonucleotides with the central XZ dinucleotide systematically mutated to all 16 sequences show complex behavior in solution, but all ten so far successfully crystallized 18-mers crystallized as A-form duplexes. The refinement protocol benefited from the recurrent use of geometries of the dinucleotide conformer (NtC) classes as refinement restraints in regions of poor electron density. The restraints are automatically generated at the dnatco.datmos.org web service and are available for download. This NtC-driven protocol significantly helped to stabilize the structure refinement. The NtC-driven refinement protocol can be adapted to other low-resolution data such as cryo-EM maps. To test the quality of the final structural models, a novel validation method based on comparison of the electron density and conformational similarity to the NtC classes was employed.

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Organizational Affiliation: 
• Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.71 kDa 
• Atom Count: 369 
• Modeled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Chom18-GT DNA	A	18	Cardiobacterium hominis

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SR	B [auth A], C [auth A]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.319 (Depositor), 0.318 (DCC) 
• R-Value Work:  0.258 (Depositor), 0.269 (DCC) 
• R-Value Observed: 0.272 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.695	α = 90
b = 37.695	β = 90
c = 89.72	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-29 
Deposition Author(s): Svoboda, J., Schneider, B., Berdar, D., Kolenko, P.

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Funding Organization	Location	Grant Number
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	D_1292120577
Czech Academy of Sciences	Czech Republic	RVO 86652036

Revision History  

• Version 1.0: 2023-03-29
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references
• Version 1.2: 2024-02-07
  Changes: Refinement description