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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 1.6 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
Find similar proteins by:  (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
Expand
  • 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

View Full Validation Report



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
  • Version 1.6: 2024-05-22
    Changes: Data collection