7S2H | pdb_00007s2h

Crystal structure of Trypanosoma cruzi glucokinase in the apo form (open conformation)

PDB DOI: https://doi.org/10.2210/pdb7S2H/pdb

Classification: TRANSFERASE
Organism(s): Trypanosoma cruzi strain CL Brener
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-09-03 Released: 2021-10-06
Deposition Author(s): Kearns, S.P., Daneshian, L., Swartz, P.D., Carey, S.M., Chruszcz, M., D'Antonio, E.L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.194 (Depositor), 0.197 (DCC)
R-Value Work:
0.165 (Depositor), 0.172 (DCC)
R-Value Observed:
0.166 (Depositor)

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

Literature

Crystal structure of Trypanosoma cruzi glucokinase in the apo form (open conformation)

Kearns, S.P., Daneshian, L., Swartz, P.D., Carey, S.M., Chruszcz, M., D'Antonio, E.L.

To be published.

Macromolecule Content

Total Structure Weight: 84.86 kDa
Atom Count: 6,257
Modeled Residue Count: 737
Deposited Residue Count: 762
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucokinase 1, putative	A, B	381	Trypanosoma cruzi strain CL Brener	Mutation(s): 0 Gene Names: Tc00.1047053510187.100 EC: 2.7.1.2
UniProt
Find proteins for Q4E4E1 (Trypanosoma cruzi (strain CL Brener)) Explore Q4E4E1 Go to UniProtKB: Q4E4E1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4E4E1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.194 (Depositor), 0.197 (DCC)
R-Value Work: 0.165 (Depositor), 0.172 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.304	α = 90
b = 78.92	β = 101.3
c = 76.847	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-10-06

Deposition Author(s):

D'Antonio, E.L.

Funding Organization	Location	Grant Number
Other government		University of South Carolina, Office of the Vice President for Research, Magellan Program

Revision History (Full details and data files)

Version 1.0: 2021-10-06
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.