4NT9

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.705 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of an L,D-carboxypeptidase DacB from Streptococcus pneumonia

Yang, Y.H.Zhang, J.Jiang, Y.L.Zhou, C.Z.Chen, Y.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
B, A, C
219Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 0 
Find proteins for A0A0H2UP74 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2UP74
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A, B, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.705 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.110α = 90.00
b = 68.080β = 108.41
c = 80.350γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
ADSCdata collection
REFMACrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release