7R7M

Crystal structure of Triosephosphate isomerase from Candidate division Katanobacteria (WWE3) bacterium

PDB DOI: https://doi.org/10.2210/pdb7R7M/pdb

Classification: ISOMERASE
Organism(s): candidate division WWE3 bacterium RAAC2_WWE3_1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-24 Released: 2022-07-06
Deposition Author(s): Vickers, C.J., Patrick, W.M., Fraga, D.
Funding Organization(s): Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.211
R-Value Work: 0.151
R-Value Observed: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of WweTPI - Candidate division WWE3

Vickers, C.J., Patrick, W.M., Fraga, D.

To be published.

Macromolecule Content

Total Structure Weight: 47.68 kDa
Atom Count: 3,686
Modelled Residue Count: 432
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	216	candidate division WWE3 bacterium RAAC2_WWE3_1	Mutation(s): 0 Gene Names: DIU24_00595 EC: 5.3.1.1
UniProt
Find proteins for A0A656PMZ5 (candidate division WWE3 bacterium) Explore A0A656PMZ5 Go to UniProtKB: A0A656PMZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A656PMZ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.211
R-Value Work: 0.151
R-Value Observed: 0.154
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.461	α = 90
b = 39.499	β = 103.333
c = 78.149	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Funding Organization	Location	Grant Number
Royal Society of New Zealand	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2022-07-06
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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 R01GM133198.