6FU2 | pdb_00006fu2

ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRPP and ATP

PDB DOI: https://doi.org/10.2210/pdb6FU2/pdb

Classification: TRANSFERASE
Organism(s): Psychrobacter arcticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-26 Released: 2018-10-24
Deposition Author(s): Alphey, M.S., Ge, Y., Fisher, G., Czekster, C.M., Naismith, J.H., da Silva, R.G.
Funding Organization(s): Biotechnology and Biological Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free:
0.243 (Depositor), 0.247 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Catalytic and Anticatalytic Snapshots of a Short-Form ATP Phosphoribosyltransferase

Alphey, M.S., Fisher, G., Hirschi, J.S., Stroek, R., Ge, Y., Gould, E.R., Czekster, C.M., Liu, H., Florence, G.J., Vetticatt, M.J., Naismith, J.H., da Silva, R.G.

(2018) ACS Catal

DOI: https://doi.org/10.1021/acscatal.8b00867

Macromolecule Content

Total Structure Weight: 138.95 kDa
Atom Count: 9,238
Modeled Residue Count: 1,169
Deposited Residue Count: 1,240
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase regulatory subunit	A, B	388	Psychrobacter arcticus	Mutation(s): 0 Gene Names: hisZ, Psyc_0676
UniProt
Find proteins for Q4FTX3 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4)) Explore Q4FTX3 Go to UniProtKB: Q4FTX3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4FTX3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase	C, D	232	Psychrobacter arcticus	Mutation(s): 0 Gene Names: hisG, Psyc_1903 EC: 2.4.2.17
UniProt
Find proteins for Q4FQF7 (Psychrobacter arcticus (strain DSM 17307 / VKM B-2377 / 273-4)) Explore Q4FQF7 Go to UniProtKB: Q4FQF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q4FQF7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain L [auth D] MOL2 format, chain G [auth C] MOL2 format, chain L [auth D] mmCIF format, chain G [auth C] mmCIF format, chain L [auth D]	G [auth C], L [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth C] Focus chain L [auth D] Interactions & Density Focus chain G [auth C] Focus chain L [auth D]
PRP Query on PRP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain F [auth C] MOL2 format, chain K [auth D] MOL2 format, chain F [auth C] mmCIF format, chain K [auth D] mmCIF format, chain F [auth C]	F [auth C], K [auth D]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C₅ H₁₃ O₁₄ P₃ PQGCEDQWHSBAJP-TXICZTDVSA-N		Interactions Focus chain F [auth C] Focus chain K [auth D] Interactions & Density Focus chain F [auth C] Focus chain K [auth D]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain M [auth D] SDF format, chain E [auth B] MOL2 format, chain J [auth C] MOL2 format, chain M [auth D] MOL2 format, chain E [auth B] mmCIF format, chain J [auth C] mmCIF format, chain M [auth D] mmCIF format, chain E [auth B]	E [auth B], J [auth C], M [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain E [auth B] Focus chain J [auth C] Focus chain M [auth D] Interactions & Density Focus chain E [auth B] Focus chain J [auth C] Focus chain M [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain H [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C]	H [auth C], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth C] Interactions & Density Focus chain H [auth C] Focus chain I [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.243 (Depositor), 0.247 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.72	α = 90
b = 146.2	β = 102.16
c = 94.51	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M010996/1

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description, Structure summary