7R7M | pdb_00007r7m

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 (Depositor), 0.266 (DCC)
R-Value Work:
0.151 (Depositor)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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
Modeled Residue Count: 432
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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 (Depositor), 0.266 (DCC)
R-Value Work: 0.151 (Depositor)
R-Value Observed: 0.154 (Depositor)

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

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Ligand Structure Quality Assessment

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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

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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.