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Crystal structure of glycerophosphodiester phosphodiesterase (GDPD) (TM1621) from Thermotoga maritima at 1.60 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of a glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima (TM1621) at 1.60 A resolution.

Santelli, E., Schwarzenbacher, R., McMullan, D., Biorac, T., Brinen, L.S., Canaves, J.M., Cambell, J., Dai, X., Deacon, A.M., Elsliger, M.A., Eshagi, S., Floyd, R., Godzik, A., Grittini, C., Grzechnik, S.K., Jaroszewski, L., Karlak, C., Klock, H.E., Koesema, E., Kovarik, J.S., Kreusch, A., Kuhn, P., Lesley, S.A., McPhillips, T.M., Miller, M.D., Morse, A., Moy, K., Ouyang, J., Page, R., Quijano, K., Rezezadeh, F., Robb, A., Stevens, R.C., van den Bedem, H., Velasquez, J., Vincent, J., von Delft, F., Wang, X., West, B., Wolf, G., Xu, Q., Hodgson, K.O., Wooley, J., Wilson, I.A.

(2004) Proteins 56: 167-170


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
glycerophosphodiester phosphodiesterase234Thermotoga maritimaMutation(s): 0 
Gene Names: TM1621
EC: 3.1.4.46
UniProt
Find proteins for Q9X1V6 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1V6 
Go to UniProtKB:  Q9X1V6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1V6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA
Download Ideal Coordinates CCD File 
B [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.41α = 90
b = 41.79β = 90
c = 51.72γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEmodel building
SOLVEphasing
ARP/wARPmodel building
REFMACrefinement
RESOLVEphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-01
    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: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-07-18
    Changes: Data collection, Database references
  • Version 1.5: 2023-01-25
    Changes: Database references, Derived calculations