1VPA | pdb_00001vpa

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from Thermotoga maritima at 2.67 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VPA/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-14 Released: 2004-11-02 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from Thermotoga maritima at 2.67 A resolution

Joint Center for Structural Genomics (JCSG)

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)

Macromolecule Content

• Total Structure Weight: 54.88 kDa 
• Atom Count: 3,621 
• Modelled Residue Count: 441 
• Deposited Residue Count: 468 
• 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	234	Thermotoga maritima	Mutation(s): 0  Gene Names: TM1393, ispD EC: 2.7.7.60
UniProt
Find proteins for Q9X1B3 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X1B3  Go to UniProtKB:  Q9X1B3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CTP	D [auth A], G [auth B]	CYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O14 P3 PCDQPRRSZKQHHS-XVFCMESISA-N
ACY	E [auth A], H [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.248 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VPA

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.23	α = 90
b = 144.23	β = 90
c = 53.724	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-11-02 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2004-11-02
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-20
  Changes: Data collection, Refinement description