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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free:
0.165 (Depositor), 0.164 (DCC)
R-Value Work:
0.142 (Depositor), 0.141 (DCC)
R-Value Observed:
0.144 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7URP

This is version 1.1 of the entry. See complete history.

Literature

Structures of cohesin modules from Sca5 of Ruminococcus bromii

Cerqueira, F., Koropatkin, N.

To be published.

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

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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	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.03 Å
R-Value Free: 0.165 (Depositor), 0.164 (DCC)
R-Value Work: 0.142 (Depositor), 0.141 (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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-05-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.