3OKR | pdb_00003okr

Structure of Mtb apo 2-C-methyl-D-erythritol 4-phosphate cytidyltransferase (IspD)

• PDB DOI: https://doi.org/10.2210/pdb3OKR/pdb

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


• Deposited: 2010-08-25 Released: 2010-10-06 
• Deposition Author(s): Sacchettini, J.C., Reddy, M.C.M., Bruning, J.B., Thurman, C., TB Structural Genomics Consortium (TBSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.278 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

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

Sacchettini, J.C., Reddy, M.C.M., Bruning, J.B., Thurman, C.

To be published.

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97 kDa 
• Atom Count: 5,771 
• Modeled Residue Count: 817 
• Deposited Residue Count: 931 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase	A, B, C, D	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heptamer peptide	E [auth F]	7	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: ispD, Rv3582c, MT3688, MTCY06G11.29c

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.278 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.081	α = 104.18
b = 60.268	β = 110.52
c = 74.512	γ = 88.68

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Sacchettini, J.C., Reddy, M.C.M., Bruning, J.B., Thurman, C., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-09-05
  Changes: Derived calculations
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description