5AOZ | pdb_00005aoz

High resolution SeMet structure of the third cohesin from Ruminococcus flavefaciens scaffoldin protein, ScaB

PDB DOI: https://doi.org/10.2210/pdb5AOZ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Ruminococcus flavefaciens FD-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-09-14 Released: 2016-09-28
Deposition Author(s): Bule, P., Carvalho, A.L., Santos, H., Fontes, C.M.G.A., Najmudin, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free:
0.142 (Depositor), 0.161 (DCC)
R-Value Work:
0.118 (Depositor), 0.138 (DCC)
R-Value Observed:
0.120 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5AOZ

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

Literature

Structural Characterization of the Third Cohesin from Ruminococcus Flavefaciens Scaffoldin Protein, Scab

Bule, P., Carvalho, A.L., Santos, H., Fontes, C.M.G.A., Najmudin, S.

To be published.

Macromolecule Content

Total Structure Weight: 18.37 kDa
Atom Count: 1,330
Modeled Residue Count: 141
Deposited Residue Count: 169
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE CELLULOSOMAL SCAFFOLDIN PROTEIN	A	169	Ruminococcus flavefaciens FD-1	Mutation(s): 0
UniProt
Find proteins for A0AEF4 (Ruminococcus flavefaciens) Explore A0AEF4 Go to UniProtKB: A0AEF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0AEF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.14 Å
R-Value Free: 0.142 (Depositor), 0.161 (DCC)
R-Value Work: 0.118 (Depositor), 0.138 (DCC)
R-Value Observed: 0.120 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.427	α = 90
b = 60.427	β = 90
c = 86.509	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-09-28

Deposition Author(s):

Fontes, C.M.G.A.

Revision History (Full details and data files)

Version 1.0: 2016-09-28
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Other, Structure summary

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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.