6FTT

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

PDB DOI: https://doi.org/10.2210/pdb6FTT/pdb

Classification: TRANSFERASE
Organism(s): Psychrobacter arcticus 273-4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-23 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: 2.29 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.193 (Depositor), 0.200 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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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: 275.56 kDa
Atom Count: 18,887
Modelled Residue Count: 2,346
Deposited Residue Count: 2,480
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase regulatory subunit	A, B [auth C], C [auth B], D	388	Psychrobacter arcticus 273-4	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4FTX3
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP phosphoribosyltransferase	E, F [auth H], G, H [auth F]	232	Psychrobacter arcticus 273-4	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4FQF7
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRP (Subject of Investigation/LOI) Query on PRP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain R [auth E] SDF format, chain T [auth H] SDF format, chain W [auth G] MOL2 format, chain AA [auth F] MOL2 format, chain R [auth E] MOL2 format, chain T [auth H] MOL2 format, chain W [auth G] mmCIF format, chain AA [auth F] mmCIF format, chain R [auth E] mmCIF format, chain T [auth H] mmCIF format, chain W [auth G]	AA [auth F], R [auth E], T [auth H], W [auth G]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C₅ H₁₃ O₁₄ P₃ PQGCEDQWHSBAJP-TXICZTDVSA-N		Interactions Focus chain AA [auth F] Focus chain R [auth E] Focus chain T [auth H] Focus chain W [auth G] Interactions & Density Focus chain AA [auth F] Focus chain R [auth E] Focus chain T [auth H] Focus chain W [auth G]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain J [auth A] SDF format, chain L [auth C] SDF format, chain N [auth B] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth H] SDF format, chain V [auth H] SDF format, chain X [auth G] SDF format, chain Y [auth G] SDF format, chain Z [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth G] MOL2 format, chain Z [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain L [auth C] mmCIF format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth H] mmCIF format, chain V [auth H] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth G] mmCIF format, chain Z [auth G]	BA [auth F] J [auth A] L [auth C] N [auth B] P [auth D] BA [auth F], J [auth A], L [auth C], N [auth B], P [auth D], Q [auth D], S [auth E], U [auth H], V [auth H], X [auth G], Y [auth G], Z [auth G]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth F] Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth H] Focus chain V [auth H] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth F] Focus chain J [auth A] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth H] Focus chain V [auth H] Focus chain X [auth G] Focus chain Y [auth G] Focus chain Z [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain M [auth B] SDF format, chain O [auth D] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth B] MOL2 format, chain O [auth D] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth B] mmCIF format, chain O [auth D]	I [auth A], K [auth C], M [auth B], O [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth B] Focus chain O [auth D] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth B] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.193 (Depositor), 0.200 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.77	α = 90
b = 147.79	β = 103.05
c = 98.94	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

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