1Y7M

Crystal Structure of the B. subtilis YkuD protein at 2 A resolution

Structural Biology Knowledgebase: 1Y7M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.211

Literature

Macromolecules
Sequence Display for 1Y7M

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 35985.10

Macromolecule Entities
Molecule Chains Length Organism Details
hypothetical protein BSU14040 A, B 164 Bacillus subtilis EC#: 2 IUBMB
Mutation: M1M, M76M, K117A, Q118A, M142M
Gene Name(s): ykuD BSU14040
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CD
Query on CD

A, B CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.211
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.28 α = 90.00
b = 63.91 β = 90.00
c = 93.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-09
  • Released Date: 2005-03-01
  • Deposition author(s): Bielnicki, J.A., Devedjiev, Y., Derewenda, U., Dauter, Z., Joachimiak, A., Derewenda, Z.S., Midwest Center for Structural Genomics (MCSG)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4