3VFL | pdb_00003vfl

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 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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.

Macromolecule Content 

  • Total Structure Weight: 68.81 kDa 
  • Atom Count: 5,014 
  • Modeled Residue Count: 614 
  • Deposited Residue Count: 622 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B
311Streptococcus pneumoniae SP3-BS71Mutation(s): 0 
Gene Names: CGSSp3BS71_00085, dapA
EC: 4.2.1.52

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 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.165 (Depositor), 0.165 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
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



View more in-depth experimental data

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