3VFL

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure, Function, Stability and Knockout Phenotype of Dihydrodipicolinate Synthase from Streptococcus pneumoniae

Dogovski, C.Gorman, M.A.Ketaren, N.E.Praszkier, J.Bryant, G.Yang, J.Griffin, M.D.W.Pearce, F.G.Bhargava, S.K.Dobson, R.C.J.Hutton, C.A.Gerrard, J.A.Robins-Browne, R.M.Jameson, G.B.Parker, M.W.Perugini, M.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B
311Streptococcus pneumoniae SP3-BS71Mutation(s): 0 
Gene Names: CGSSp3BS71_00085dapA
EC: 4.2.1.52
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
I [auth B],
J [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.168 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.357α = 90
b = 105.332β = 90
c = 105.51γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2013-06-12 
  • Deposition Author(s): Gorman, M.A.
  • This entry supersedes: 3H5D

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description