3GVE

Crystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Calcineurin-like Phosphoesterase from Bacillus subtilis

Kim, Y.Marshall, N.Cobb, G.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YfkN protein
A, B
341Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yfkN
Find proteins for O34313 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34313
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CIT
Query on CIT

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Download CCD File 
A, B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.163 
  • R-Value Work: 0.154 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 67.091α = 90.00
b = 92.505β = 89.94
c = 50.316γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
SOLVEphasing
SBC-Collectdata collection
SHELXCDphasing
DMphasing
DMmodel building
PHENIXrefinement
MLPHAREphasing
RESOLVEphasing
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
RESOLVEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description