7URP | pdb_00007urp

Second cohesin module from Sca5 of Ruminococcus bromii

• PDB DOI: https://doi.org/10.2210/pdb7URP/pdb

• Classification: PROTEIN BINDING
• Organism(s): Ruminococcus bromii L2-63
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2022-04-22 Released: 2023-05-03 
• Deposition Author(s): Cerqueira, F., Koropatkin, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.144 (Depositor) 

Literature

Structures of cohesin modules from Sca5 of Ruminococcus bromii

Cerqueira, F., Koropatkin, N.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 17.17 kDa 
• Atom Count: 1,452 
• Modeled Residue Count: 159 
• Deposited Residue Count: 160 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleases G and E	A	160	Ruminococcus bromii L2-63	Mutation(s): 0  Gene Names: RBL236_00045

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free:  0.165 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.144 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.57	α = 90
b = 30.05	β = 94.53
c = 49.94	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-05-03 
Deposition Author(s): Cerqueira, F., Koropatkin, N.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-05-03
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection