1H3M | pdb_00001h3m

Structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthetase

• PDB DOI: https://doi.org/10.2210/pdb1H3M/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli BL21(DE3)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2002-09-10 Released: 2003-08-01 
• Deposition Author(s): Kemp, L.E., Bond, C.S., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.333 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

Structure of a Tetragonal Crystal Form of Escherichia Coli 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase

Kemp, L.E., Bond, C.S., Hunter, W.N.

(2003) Acta Crystallogr D Biol Crystallogr 59: 607

• PubMed: 12595740 
• DOI: https://doi.org/10.1107/s090744490202365x
• Primary Citation Related Structures: 
  1H3M


• PubMed Abstract: 
  

  2-C-Methyl-D-erythritol 4-phosphate cytidylyltransferase is an essential enzyme in the mevalonate-independent pathway of isoprenoid biosynthesis. The structure of a tetragonal crystal form has been solved by molecular replacement and refined to 2.4 A resolution. Structure and sequence comparisons suggest that the enzyme is a suitable target for a structure-based approach to the development of novel broad-spectrum antibiotics. However, the absence of ligands in the enzyme active site together with the moderate resolution of the structure indicates that this tetragonal crystal form is inferior to that of a previously reported highly ordered monoclinic form [Richard et al. (2001), Nature Struct. Biol. 8, 641-647].

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Organizational Affiliation: 
• Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 51.62 kDa 
• Atom Count: 3,414 
• Modeled Residue Count: 433 
• Deposited Residue Count: 470 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE	A, B	235	Escherichia coli BL21(DE3)	Mutation(s): 1  EC: 2.7.7.60
UniProt
Find proteins for Q46893 (Escherichia coli (strain K12)) Explore Q46893  Go to UniProtKB:  Q46893

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
N2P	D [auth A]	PENTANE-1,5-DIAMINE C5 H14 N2 VHRGRCVQAFMJIZ-UHFFFAOYSA-N
CL	C [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.333 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.604	α = 90
b = 73.604	β = 90
c = 175.562	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-01 
Deposition Author(s): Kemp, L.E., Bond, C.S., Hunter, W.N.

Revision History  

• Version 1.0: 2003-08-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.4: 2024-11-13
  Changes: Structure summary