3NWG | pdb_00003nwg

The crystal structure of a microcomparments protein from Desulfitobacterium hafniense DCB

• PDB DOI: https://doi.org/10.2210/pdb3NWG/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Desulfitobacterium hafniense DCB-2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-09 Released: 2010-09-22 
• Deposition Author(s): Fan, Y., Volkart, L., Gu, M., Axen, S., Greenleaf, W.B., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.283 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Literature

Structure of a PduT homolog from a novel bacterial microcompartment

Greenleaf, W.B., Fan, Y., Axen, S., Volkart, L., Gu, M., Joachimiak, A., Kerfeld, C.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.23 kDa 
• Atom Count: 1,341 
• Modelled Residue Count: 180 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Microcompartments protein	A	182	Desulfitobacterium hafniense DCB-2	Mutation(s): 0  Gene Names: Dhaf_0360
UniProt
Find proteins for B8G1Q4 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8G1Q4  Go to UniProtKB:  B8G1Q4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.283 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.862	α = 90
b = 104.862	β = 90
c = 81.309	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
RESOLVE	model building
HKL-3000	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Fan, Y., Volkart, L., Gu, M., Axen, S., Greenleaf, W.B., Kerfeld, C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary