7Z67

Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with a adenosine nucleotide analog.

• PDB DOI: https://doi.org/10.2210/pdb7Z67/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2022-03-11 Released: 2022-03-23 
• Deposition Author(s): Hothorn, M., Martinez, J.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.244 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 

Literature

Structural and biological insight into the plant unique multimodular triphosphosphate tunnel metalloenzymes of Arabidopsis thaliana

Pesquera, M., Martinez, J., Wang, K., Hofmann, M., Loubery, S., Steensma, P., Hothorn, M., Fitzpatrick, T.B.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 46.42 kDa 
• Atom Count: 3,228 
• Modelled Residue Count: 393 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase TTM1	A	396	Arabidopsis thaliana	Mutation(s): 0  Gene Names: TTM1, At1g73980, F2P9.15 EC: 3.6.1.1
UniProt
Find proteins for Q9C9B9 (Arabidopsis thaliana) Explore Q9C9B9  Go to UniProtKB:  Q9C9B9

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP (Subject of Investigation/LOI)	D [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
CIT	B [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.244 
• R-Value Work: 0.219 
• R-Value Observed: 0.220 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.37	α = 90
b = 93.37	β = 90
c = 266.327	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELXCD	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-03-23 
Deposition Author(s): Hothorn, M., Martinez, J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	310856

Revision History  

• Version 1.0: 2022-03-23
  Type: Initial release