5CD6 | pdb_00005cd6

Crystal structure of a TPR-domain containing protein (BDI_1685) from Parabacteroides distasonis ATCC 8503 at 2.26 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5CD6/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Parabacteroides distasonis ATCC 8503
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-03 Released: 2015-07-29 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 
  0.208 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.176 (Depositor) 

Literature

Crystal structure of a TPR-domain containing protein (BDI_1685) from Parabacteroides distasonis ATCC 8503 at 2.26 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 201.5 kDa 
• Atom Count: 15,631 
• Modeled Residue Count: 1,725 
• Deposited Residue Count: 1,740 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TPR-domain containing protein	A, B, C	580	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_1685
UniProt
Find proteins for A6LCM3 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LCM3  Go to UniProtKB:  A6LCM3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth B], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	D [auth A], E [auth A], G [auth B], I [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free:  0.208 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.176 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35CD6

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.48	α = 90
b = 167.48	β = 90
c = 312.23	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
SOLVE	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Derived calculations, Source and taxonomy
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.3: 2024-10-30
  Changes: Data collection, Structure summary