1XM5

Crystal structure of metal-dependent hydrolase ybeY from E. coli, Pfam UPF0054

Structural Biology Knowledgebase: 1XM5 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.234

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XM5

Classification: STRUCTURAL GENOMICS UNKNOWN FUNCTION

Total Structure Weight: 70393.69

Macromolecule Entities
Molecule Chains Length Organism Details
Hypothetical UPF0054 protein ybeY A, B, C, D 155 Escherichia coli Gene Name(s): ybeY b0659 JW0656
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NI
Query on NI

A, B, C, D NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.273
  • R-Value Work: 0.234
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 46.07 α = 90.00
b = 119.61 β = 90.00
c = 132.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-10-01
  • Released Date: 2004-10-12
  • Deposition author(s): Fedorov, A.A., Fedorov, E.V., Shi, W., Ramagopal, U.A., Thirumuruhan, R., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History

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