7RMN | pdb_00007rmn

Crystal structure of triosephosphate isomerase from Verrucomicrobium spinosum

PDB DOI: https://doi.org/10.2210/pdb7RMN/pdb

Classification: ISOMERASE
Organism(s): Verrucomicrobium spinosum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-27 Released: 2022-08-10
Deposition Author(s): Vickers, C.J., Fraga, D., Patrick, W.M.
Funding Organization(s): Royal Society of New Zealand

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free:
0.179 (Depositor), 0.178 (DCC)
R-Value Work:
0.164 (Depositor), 0.164 (DCC)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of VspTPI - Verrucomicrobium spinosum triosephoshate isomerase

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

To be published.

Macromolecule Content

Total Structure Weight: 59.27 kDa
Atom Count: 4,889
Modeled Residue Count: 533
Deposited Residue Count: 542
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	271	Verrucomicrobium spinosum	Mutation(s): 0 EC: 5.3.1.1
UniProt
Find proteins for A0A979HMP0 (Verrucomicrobium spinosum) Explore A0A979HMP0 Go to UniProtKB: A0A979HMP0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A979HMP0
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.21 Å
R-Value Free: 0.179 (Depositor), 0.178 (DCC)
R-Value Work: 0.164 (Depositor), 0.164 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.99	α = 90
b = 64.118	β = 100.787
c = 94.215	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-10

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: 2022-08-10
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.