5BMQ

Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of L,D-transpeptidases (Yku)

Chang, C.Bigelow, L.Clancy, S.Joachimiak, A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ErfK/YbiS/YcfS/YnhG family protein
A
243Stackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21)
Find proteins for D3Q1D9 (Stackebrandtia nassauensis (strain DSM 44728 / NRRL B-16338 / NBRC 102104 / LLR-40K-21))
Go to UniProtKB:  D3Q1D9
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DIO
Query on DIO

Download SDF File 
Download CCD File 
A
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.154 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 143.356α = 90.00
b = 143.356β = 90.00
c = 143.356γ = 90.00
Software Package:
Software NamePurpose
HKL-3000phasing
SCALEPACKdata scaling
SBC-Collectdata collection
HKL-3000data reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release