4WK5 | pdb_00004wk5

Crystal structure of a Isoprenoid Synthase family member from Thermotoga neapolitana DSM 4359, target EFI-509458

• PDB DOI: https://doi.org/10.2210/pdb4WK5/pdb

• Classification: TRANSFERASE
• Organism(s): Thermotoga neapolitana DSM 4359
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-10-01 Released: 2014-11-19 
• Deposition Author(s): Toro, R., Bhosle, R., Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Poulter, C.D., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal structure of a Isoprenoid Synthase family member from Thermotoga neapolitana DSM 4359, target EFI-509458

Toro, R., Bhosle, R., Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Poulter, C.D., Almo, S.C., Enzyme Function Initiative (EFI)

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: 33.48 kDa 
• Atom Count: 2,236 
• Modeled Residue Count: 256 
• Deposited Residue Count: 294 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranyltranstransferase	A	294	Thermotoga neapolitana DSM 4359	Mutation(s): 0  Gene Names: CTN_0526
UniProt
Find proteins for B9K6W9 (Thermotoga neapolitana (strain ATCC 49049 / DSM 4359 / NBRC 107923 / NS-E)) Explore B9K6W9  Go to UniProtKB:  B9K6W9

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.209 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.223	α = 90
b = 118.458	β = 90
c = 79.685	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-19 
Deposition Author(s): Toro, R., Bhosle, R., Vetting, M.W., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hillerich, B., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Poulter, C.D., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2014-11-19
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Other, Refinement description, Source and taxonomy
• Version 1.2: 2023-12-27
  Changes: Data collection, Database references, Refinement description