7Z66 | pdb_00007z66

Crystal structure of the tandem kinase & triphosphate tunnel metalloenzyme domain module of the TTM1 protein from Arabidoposis thaliana in complex with inorganic phosphate and citric acid.

PDB DOI: https://doi.org/10.2210/pdb7Z66/pdb

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

Deposited: 2022-03-11 Released: 2022-04-06
Deposition Author(s): Hothorn, M., Martinez, J.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.235 (Depositor), 0.239 (DCC)
R-Value Work:
0.213 (Depositor), 0.222 (DCC)
R-Value Observed:
0.214 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 7Z66

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 45.96 kDa
Atom Count: 3,221
Modeled Residue Count: 393
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase TTM1	A [auth AAAA]	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C9B9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT (Subject of Investigation/LOI) Query on CIT Download:Ideal Coordinates CCD File SDF format, chain B [auth AAAA] MOL2 format, chain B [auth AAAA] mmCIF format, chain B [auth AAAA]	B [auth AAAA]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain B [auth AAAA] Interactions & Density Focus chain B [auth AAAA]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth AAAA] MOL2 format, chain D [auth AAAA] mmCIF format, chain D [auth AAAA]	D [auth AAAA]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth AAAA] Interactions & Density Focus chain D [auth AAAA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain C [auth AAAA] MOL2 format, chain C [auth AAAA] mmCIF format, chain C [auth AAAA]	C [auth AAAA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth AAAA] Interactions & Density Focus chain C [auth AAAA]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.235 (Depositor), 0.239 (DCC)
R-Value Work: 0.213 (Depositor), 0.222 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.712	α = 90
b = 93.712	β = 90
c = 267.744	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-06

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2022-04-06
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.