3Q80

Structure of Mtb 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD) Complexed with CDP-ME

• PDB DOI: https://doi.org/10.2210/pdb3Q80/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-05 Released: 2011-05-04 
• Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Thurman, C., Ioerger, T.R., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 

Starting Model: experimental

Literature

Crystal Structure of Mycobacterium tuberculosis 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD): a candidate antitubercular drug target

Reddy, M.C.M., Bruning, J.B., Thurman, C., Ioerger, T.R., Sacchettini, J.C.

(2011) Proteins 

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 PISA (software)

Macromolecule Content

• Total Structure Weight: 49.36 kDa 
• Atom Count: 3,664 
• Modelled Residue Count: 436 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 4-phosphate cytidyltransferase	A, B	231	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ispD, Rv3582c, MT3688, MTCY06G11.29c EC: 2.7.7.60
UniProt
Find proteins for P9WKG9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKG9  Go to UniProtKB:  P9WKG9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDM	C [auth A], G [auth B]	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL C14 H25 N3 O14 P2 YFAUKWZNPVBCFF-XHIBXCGHSA-N
CL	E [auth A], F [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.165 
• R-Value Observed: 0.167 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.581	α = 90
b = 92.668	β = 90
c = 146.421	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-04 
Deposition Author(s): Reddy, M.C.M., Bruning, J.B., Thurman, C., Ioerger, T.R., Sacchettini, J.C., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2011-05-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2014-11-12
  Changes: Structure summary
• Version 1.3: 2017-11-08
  Changes: Refinement description
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description