7R9B

Crystal structure of Triosephosphate isomerase from Candidatus Roizmanbacteria

PDB DOI: https://doi.org/10.2210/pdb7R9B/pdb

Classification: ISOMERASE
Organism(s): Candidatus Roizmanbacteria
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-06-28 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: 2.20 Å
R-Value Free: 0.230
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of Triosephosphate isomerase from Candidatus Roizmanbacteria

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

To be published.

Macromolecule Content

Total Structure Weight: 24.77 kDa
Atom Count: 1,779
Modelled Residue Count: 223
Deposited Residue Count: 223
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A	223	Candidatus Roizmanbacteria	Mutation(s): 0 Gene Names: A3B50_02135 EC: 5.3.1.1
UniProt
Find proteins for A0A1F7J4N7 (Candidatus Roizmanbacteria bacterium RIFCSPLOWO2_01_FULL_40_42) Explore A0A1F7J4N7 Go to UniProtKB: A0A1F7J4N7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1F7J4N7
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 B [auth A] MOL2 format, chain B [auth A]	B [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.230
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.937	α = 90
b = 108.937	β = 90
c = 41.015	γ = 120

Software Package:

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

Structure Validation

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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.