4RGP | pdb_00004rgp

Crystal Structure of Uncharacterized CRISPR/Cas System-associated Protein Csm6 from Streptococcus mutans

• PDB DOI: https://doi.org/10.2210/pdb4RGP/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Streptococcus mutans UA159
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-30 Released: 2014-12-24 
• Deposition Author(s): Kim, Y., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Crystal Structure of Uncharacterized CRISPR/Cas System-associated Protein Csm6 from Streptococcus mutans

Kim, Y., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.95 kDa 
• Atom Count: 4,492 
• Modeled Residue Count: 510 
• Deposited Residue Count: 514 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm6_III-A	A, B	257	Streptococcus mutans UA159	Mutation(s): 0
UniProt
Find proteins for Q8DTU7 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore Q8DTU7  Go to UniProtKB:  Q8DTU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	K [auth B], L [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	C [auth A], D [auth A], E [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.243 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.511	α = 90
b = 78.238	β = 90
c = 92.269	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Kim, Y., Li, H., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary