7RCQ | pdb_00007rcq

Crystal structure of triosephosphate isomerase from Ktedonobacter racemifer

PDB DOI: https://doi.org/10.2210/pdb7RCQ/pdb

Classification: ISOMERASE
Organism(s): Ktedonobacter racemifer
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-07 Released: 2022-07-13
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: 1.70 Å
R-Value Free:
0.189 (Depositor), 0.190 (DCC)
R-Value Work:
0.158 (Depositor), 0.160 (DCC)
R-Value Observed:
0.159 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of Triosephosphate isomerase from Ktedonobacter racemifer

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

To be published.

Macromolecule Content

Total Structure Weight: 29.26 kDa
Atom Count: 2,123
Modeled Residue Count: 251
Deposited Residue Count: 269
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	269	Ktedonobacter racemifer	Mutation(s): 0 Gene Names: tpiA, Krac_9127 EC: 5.3.1.1
UniProt
Find proteins for D6TR79 (Ktedonobacter racemifer DSM 44963) Explore D6TR79 Go to UniProtKB: D6TR79
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D6TR79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 (Subject of Investigation/LOI) Query on NO3 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.189 (Depositor), 0.190 (DCC)
R-Value Work: 0.158 (Depositor), 0.160 (DCC)
R-Value Observed: 0.159 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.58	α = 90
b = 54.741	β = 115.196
c = 74.843	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-07-13

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: 2022-07-13
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 R01GM157729.