2F07 | pdb_00002f07

Crystal Structure of YvdT from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb2F07/pdb

• Classification: TRANSCRIPTION
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-12 Released: 2006-11-21 
• Deposition Author(s): Su, X.-D., Yu, Y.-M., Nan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.255 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.238 (Depositor) 

Literature

Crystal Structure of YvdT from Bacillus subtilis

Su, X.-D., Yu, Y.-M., Nan, J.

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)

Macromolecule Content 

• Total Structure Weight: 45.62 kDa 
• Atom Count: 3,301 
• Modeled Residue Count: 393 
• Deposited Residue Count: 394 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YvdT	A, B	197	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0
UniProt
Find proteins for O07001 (Bacillus subtilis (strain 168)) Explore O07001  Go to UniProtKB:  O07001

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTB	C [auth A], D [auth B]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.255 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.238 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.608	α = 90
b = 115.608	β = 90
c = 97.032	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
SHELXS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-21 
Deposition Author(s): Su, X.-D., Yu, Y.-M., Nan, J.

Revision History  

• Version 1.0: 2006-11-21
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-03-13
  Changes: Data collection, Database references, Derived calculations