1KER

The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.175

Literature

Macromolecules
Sequence Display for 1KER

Classification: LYASE

Total Structure Weight: 80708.25

Macromolecule Entities
Molecule Chains Length Organism Details
dTDP-D-glucose 4,6-dehydratase A, B 348 Streptococcus suis EC#: 4.2.1.46 IUBMB
Gene Name(s): rmlB rfbB A6M16_03315 APQ97_03200 CWI26_07360 CWM22_07885 ERS132370_01395 ERS132374_01253 ERS132410_01682 ERS132414_00580 ERS132421_00412 ERS132431_00441 ERS132440_01438 ERS132444_01827 ERS132457_01850 ERS132458_00971 ERS132461_00211 ERS132462_01604 ERS132502_01610 ERS132531_00495 ERS132536_02274 LI88_04195
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DAU
Query on DAU

A, B 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
C16 H26 N2 O16 P2
YSYKRGRSMLTJNL-URARBOGNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.206
  • R-Value Work: 0.175
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 61.22 α = 90.00
b = 96.15 β = 90.00
c = 182.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-11-17
  • Released Date: 2002-01-25
  • Deposition author(s): Allard, S.T.M., Beis, K., Giraud, M.-F., Hegeman, A.D., Gross, J.W., Whitfield, C., Graninger, M., Messner, P., Allen, A.G., Naismith, J.H.

Revision History

  • Version 1_0: 2002-01-25

    Type: Initial release

  • Version 1_1: 2008-04-27

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Version format compliance

  • Version 1_3: 2012-05-23

    Type: Atomic model, Refinement description