3NRT

The crystal structure of putative ryanodine receptor from Bacteroides thetaiotaomicron VPI-5482

PDB DOI: https://doi.org/10.2210/pdb3NRT/pdb

Classification: structural genomics, unknown function
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2010-06-30 Released: 2010-09-15
Deposition Author(s): Wu, R., Zhang, R., James, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.201

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

he crystal strucutre of putative ryanodine receptor from Bacteroides thetaiotaomicron VPI-5482

Ruiying, W., Rongguang, Z., James, A., Andrzej, J., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 74.86 kDa
Atom Count: 4,866
Modelled Residue Count: 571
Deposited Residue Count: 618
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	103	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 0 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain G [auth A] SDF format, chain N [auth F] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain G [auth A] MOL2 format, chain N [auth F]	G [auth A] I [auth A] J [auth B] K [auth C] L [auth D] G [auth A], I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.54 Å
R-Value Free: 0.248
R-Value Work: 0.198
R-Value Observed: 0.201
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.642	α = 90
b = 89.272	β = 110.99
c = 74.697	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-09-15

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-09-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2020-09-09
Changes: Advisory, Derived calculations, Structure summary
Version 1.3: 2023-12-27
Changes: Advisory, Data collection, Database references

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Help and Resources

3NRT

The crystal structure of putative ryanodine receptor from Bacteroides thetaiotaomicron VPI-5482

he crystal strucutre of putative ryanodine receptor from Bacteroides thetaiotaomicron VPI-5482

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)