3I76

The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement

Bonanno, J.B., Dickey, M., Bain, K.T., Tang, B.K., Romero, R., Sauder, J.M., Burley, S.K., Almo, S.C.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative HAD-hydrolase yfnB
A, B, C
244Bacillus subtilisMutation(s): 0 
Gene Names: BSU07330, yfnB
UniProt
Find proteins for O06480 (Bacillus subtilis (strain 168))
Explore O06480 
Go to UniProtKB:  O06480
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO06480
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
F [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
E [auth A],
G [auth A],
I [auth B],
L [auth C]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
J [auth B],
K [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.685α = 90
b = 67.964β = 90
c = 271.404γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2018-11-21
    Changes: Data collection, Structure summary
  • Version 1.4: 2021-02-10
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-09-06
    Changes: Data collection, Database references, Refinement description