4MCJ

Crystal structure of a putative nucleoside deoxyribosyltransferase (BDI_0649) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4MCJ/pdb

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


• Deposited: 2013-08-21 Released: 2013-09-04 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 

Literature

Crystal structure of a hypothetical protein (BDI_0649) from Parabacteroides distasonis ATCC 8503 at 2.40 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 182.21 kDa 
• Atom Count: 12,676 
• Modelled Residue Count: 1,510 
• Deposited Residue Count: 1,540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E, F, G, H, I, J	154	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_0649
UniProt
Find proteins for A6L9R1 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6L9R1  Go to UniProtKB:  A6L9R1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	K [auth A], L [auth B], M [auth C], N [auth D], O [auth F], P [auth G], Q [auth H], R [auth I], S [auth J]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.212 
• R-Value Work: 0.185 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M34MCJ

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 323.85	α = 90
b = 65.629	β = 90.48
c = 102.71	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
SCALA	data scaling
BUSTER-TNT	refinement
MOSFLM	data reduction
SHELXD	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Structure summary
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations