7PEK | pdb_00007pek

Crystal structure of Triosephosphate Isomerase C216A mutant from Schizosaccharomyces pombe (SpTIM C216A)

PDB DOI: https://doi.org/10.2210/pdb7PEK/pdb

Classification: ISOMERASE
Organism(s): Schizosaccharomyces pombe 972h-
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-08-10 Released: 2022-08-24
Deposition Author(s): Romero-Romero, S., Garza-Ramos, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.206 (Depositor), 0.206 (DCC)
R-Value Work:
0.177 (Depositor), 0.176 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM C216A)

Romero-Romero, S., Garza-Ramos, G.

To be published.

Macromolecule Content

Total Structure Weight: 109.58 kDa
Atom Count: 8,363
Modeled Residue Count: 983
Deposited Residue Count: 992
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, C, D	248	Schizosaccharomyces pombe 972h-	Mutation(s): 1 Gene Names: tpi1, tpi, SPCC24B10.21 EC: 5.3.1.1
UniProt
Find proteins for P07669 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P07669 Go to UniProtKB: P07669
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07669
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] G [auth B] H [auth B] L [auth C] E [auth A], F [auth A], G [auth B], H [auth B], L [auth C], M [auth C], Q [auth D], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain Q [auth D] Focus chain R [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth C] MOL2 format, chain N [auth C] mmCIF format, chain N [auth C]	N [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain N [auth C] Interactions & Density Focus chain N [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B]	I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C]	O [auth C], P [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain O [auth C] Focus chain P [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.206 (Depositor), 0.206 (DCC)
R-Value Work: 0.177 (Depositor), 0.176 (DCC)
R-Value Observed: 0.177 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.01	α = 90
b = 149.01	β = 90
c = 99.51	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Romero-Romero, S.

Garza-Ramos, G.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2024-01-31
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.