1O1Z | pdb_00001o1z

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

• PDB DOI: https://doi.org/10.2210/pdb1O1Z/pdb

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


• Deposited: 2003-02-12 Released: 2003-04-01 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.180 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.141 (Depositor) 

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

• PubMed: 15162496 
• DOI: https://doi.org/10.1002/prot.20120
• Primary Citation Related Structures: 
  1O1Z

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Organizational Affiliation: 
• The Burnham Institute, La Jolla, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.19 kDa 
• Atom Count: 2,302 
• Modeled Residue Count: 226 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerophosphodiester phosphodiesterase	A	234	Thermotoga maritima	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.180 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.141 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31O1Z

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.41	α = 90
b = 41.79	β = 90
c = 51.72	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
RESOLVE	model building
SOLVE	phasing
ARP/wARP	model building
REFMAC	refinement
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-01 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• 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