6UAG

Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

PDB DOI: https://doi.org/10.2210/pdb6UAG/pdb

Classification: METAL TRANSPORT
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-09-10 Released: 2020-08-05
Deposition Author(s): Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.264
R-Value Work: 0.196
R-Value Observed: 0.199

wwPDB Validation 3D Report Full Report

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

Literature

Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

Wu, R., Jedrzejczak, R., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 74.98 kDa
Atom Count: 4,902
Modelled Residue Count: 568
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ryanodine receptor	A, B, C, D, E A, B, C, D, E, F	100	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1 Gene Names: BT_2247
UniProt
Find proteins for Q8A5J2 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A5J2 Go to UniProtKB: Q8A5J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A5J2
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	G, H, I, J, K G, H, I, J, K, L	2		N/A	Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D] mmCIF format, chain R [auth D]	R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth F] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth F] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth F]	M [auth A] N [auth A] O [auth B] P [auth C] Q [auth D] M [auth A], N [auth A], O [auth B], P [auth C], Q [auth D], S [auth E], T [auth E], U [auth E], V [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F]

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	G, H, I, J, K G, H, I, J, K, L	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain J Focus chain K Focus chain L

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.264
R-Value Work: 0.196
R-Value Observed: 0.199
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.968	α = 90
b = 89.391	β = 111.17
c = 74.927	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2020-08-05

Deposition Author(s):

Wu, R.

Jedrzejczak, R.

Joachimiak, A.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2020-08-05
Type: Initial release
Version 1.1: 2024-10-23
Changes: Advisory, Data collection, Database references, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

6UAG

Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

Closed Dimer of Y77A Mutant Putative Ryanodine Receptor from Bacteroides thetaiotaomicron VPI-5482

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)