9K8M | pdb_00009k8m

Hypoxanthine-guanine phosphoribosyltransferase from E. coli with HEPES

PDB DOI: https://doi.org/10.2210/pdb9K8M/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-24 Released: 2024-11-06
Deposition Author(s): Timofeev, V.I., Shevtsov, M.B., Abramchik, Y.A., Kostromina, M.A., Zayats, E.A., Kuranova, I.P., Esipov, R.S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.08 Å
R-Value Free:
0.227 (Depositor), 0.237 (DCC)
R-Value Work:
0.204 (Depositor), 0.213 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9K8M

This is version 1.0 of the entry. See complete history.

Literature

Hypoxanthine-guanine phosphoribosyltransferase from E. coli with HEPES

Timofeev, V.I., Shevtsov, M.B., Abramchik, Y.A., Kostromina, M.A., Zayats, E.A., Kuranova, I.P., Esipov, R.S.

To be published.

Macromolecule Content

Total Structure Weight: 40.27 kDa
Atom Count: 2,748
Modeled Residue Count: 335
Deposited Residue Count: 352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	A, B	176	Escherichia coli	Mutation(s): 0 Gene Names: hpt, c0154 EC: 2.4.2.8
UniProt
Find proteins for P0A9M2 (Escherichia coli (strain K12)) Explore P0A9M2 Go to UniProtKB: P0A9M2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A9M2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE 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]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		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: 2.08 Å
R-Value Free: 0.227 (Depositor), 0.237 (DCC)
R-Value Work: 0.204 (Depositor), 0.213 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.217	α = 90
b = 85.217	β = 90
c = 168.279	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Abramchik, Y.A.

Kostromina, M.A.

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.