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 (Depositor), 0.260 (DCC)
R-Value Work:
0.196 (Depositor), 0.197 (DCC)
R-Value Observed:
0.199 (Depositor)

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

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(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

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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 S [auth E] SDF format, chain U [auth E] 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 T [auth E] SDF format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain U [auth E] 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 T [auth E] MOL2 format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain U [auth E] 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 T [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 (Depositor), 0.260 (DCC)
R-Value Work: 0.196 (Depositor), 0.197 (DCC)
R-Value Observed: 0.199 (Depositor)

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

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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)