3GWH

Crystallographic Ab Initio protein solution far below atomic resolution

• PDB DOI: https://doi.org/10.2210/pdb3GWH/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-04-01 Released: 2010-04-07 
• Deposition Author(s): Rodriguez, D.D., Grosse, C., Himmel, S., Gonzalez, C., Becker, S., Sheldrick, G.M., Uson, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 

Literature

Crystallographic ab initio protein structure solution below atomic resolution

Rodriguez, D.D., Grosse, C., Himmel, S., Gonzalez, C., de Ilarduya, I.M., Becker, S., Sheldrick, G.M., Uson, I.

(2009) Nat Methods 6: 651-653

• PubMed: 19684596 
• DOI: https://doi.org/10.1038/nmeth.1365
• Primary Citation of Related Structures:  
  3GWH


• PubMed Abstract: 
  

  Ab initio macromolecular phasing has been so far limited to small proteins diffracting at atomic resolution (beyond 1.2 A) unless heavy atoms are present. We describe a general ab initio phasing method for 2 A data, based on combination of localizing model fragments such as small á-helices with Phaser and density modification with SHELXE. We implemented this approach in the program Arcimboldo to solve a 222-amino-acid structure at 1.95 A.

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Organizational Affiliation: 

Instituto de Biología Molecular de Barcelona, Barcelona Science Park, Barcelona, Spain.

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)

Macromolecule Content

• Total Structure Weight: 26.5 kDa 
• Atom Count: 1,680 
• Modelled Residue Count: 199 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional antiterminator (BglG family)	A, B	111	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU13880, glcT
UniProt
Find proteins for O31691 (Bacillus subtilis (strain 168)) Explore O31691  Go to UniProtKB:  O31691

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.241 
• R-Value Work: 0.195 
• R-Value Observed: 0.198 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.39	α = 90
b = 65.75	β = 109.58
c = 38.19	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
APEX	data collection
SAINT	data reduction
TWINABS	data scaling
Arcimboldo	phasing
PHASER	phasing
SHELXE	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-07 
Deposition Author(s): Rodriguez, D.D., Grosse, C., Himmel, S., Gonzalez, C., Becker, S., Sheldrick, G.M., Uson, I.

Revision History  

• Version 1.0: 2010-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations