3T80

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Salmonella typhimurium bound to cytidine

Seattle Structural Genomics Center for Infectious Disease (SSGCID)Staker, B.L.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
A, B, C, D, E
A, B, C, D, E, F
162Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Gene Names: ispFSTM2929
EC: 4.6.1.12
UniProt
Find proteins for Q8ZMF7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZMF7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTN
Query on CTN

Download Ideal Coordinates CCD File 
DA [auth D]
IA [auth E]
J [auth A]
NA [auth F]
Q [auth B]
DA [auth D],
IA [auth E],
J [auth A],
NA [auth F],
Q [auth B],
X [auth C]
4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
C9 H13 N3 O5
UHDGCWIWMRVCDJ-XVFCMESISA-N
POP
Query on POP

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JA [auth E],
K [auth A]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
ZN
Query on ZN

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AA [auth D]
G [auth A]
GA [auth E]
LA [auth F]
O [auth B]
AA [auth D],
G [auth A],
GA [auth E],
LA [auth F],
O [auth B],
V [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

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EA [auth D]
FA [auth D]
KA [auth E]
L [auth A]
M [auth A]
EA [auth D],
FA [auth D],
KA [auth E],
L [auth A],
M [auth A],
N [auth A],
OA [auth F],
PA [auth F],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
Y [auth C],
Z [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG
Query on MG

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BA [auth D]
CA [auth D]
H [auth A]
HA [auth E]
I [auth A]
BA [auth D],
CA [auth D],
H [auth A],
HA [auth E],
I [auth A],
MA [auth F],
P [auth B],
W [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.013α = 90
b = 147.657β = 106.38
c = 56.919γ = 90
Software Package:
Software NamePurpose
MxDCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2011-10-12
    Changes: Structure summary
  • Version 1.2: 2018-01-24
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description