2PX7

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb2PX7/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-05-14 Released: 2007-06-12 
• Deposition Author(s): Chen, L., Tsukuda, M., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Chen, L.-Q., Liu, Z.-J., Lee, D., Chang, S.-H., Nguyen, D., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 

Starting Model: experimental

Literature

Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase from Thermus thermophilus HB8.

Chen, L., Tsukuda, M., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Chen, L.-Q., Liu, Z.-J., Lee, D., Chang, S.-H., Nguyen, D., Rose, J.P., Wang, B.-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)

Macromolecule Content

• Total Structure Weight: 50.45 kDa 
• Atom Count: 3,166 
• Modelled Residue Count: 405 
• Deposited Residue Count: 472 
• 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	236	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: ispD, TTHA0171 EC: 2.7.7.60
UniProt
Find proteins for Q5SLX2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLX2  Go to UniProtKB:  Q5SLX2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.248 
• R-Value Work: 0.227 
• R-Value Observed: 0.228 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.084	α = 90
b = 104.084	β = 90
c = 107.76	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-12 
Deposition Author(s): Chen, L., Tsukuda, M., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Chen, L.-Q., Liu, Z.-J., Lee, D., Chang, S.-H., Nguyen, D., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-05
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Refinement description