4ZFN | pdb_00004zfn

Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus containing GMP complexed in two different ways together with one or two MG2+

PDB DOI: https://doi.org/10.2210/pdb4ZFN/pdb

Classification: TRANSFERASE
Organism(s): Saccharolobus solfataricus P2
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-04-21 Released: 2015-04-29
Deposition Author(s): Christoffersen, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.180 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Sulfolobus solfataricus P2

Christoffersen, S., Hansen, M.R., Jensen, K.S., Larsen, S., Jensen, K.F.

To be published.

Macromolecule Content

Total Structure Weight: 42.36 kDa
Atom Count: 3,346
Modeled Residue Count: 350
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine phosphoribosyltransferase (GpT-2)	A, B	179	Saccharolobus solfataricus P2	Mutation(s): 0 Gene Names: gpT-2, SSO2424 EC: 2.4.2
UniProt
Find proteins for Q97W22 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W22 Go to UniProtKB: Q97W22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97W22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5GP Query on 5GP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	GUANOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₈ P RQFCJASXJCIDSX-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	D [auth A], G [auth B], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.180 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.467	α = 90
b = 74.467	β = 90
c = 143.527	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-04-29

Deposition Author(s):

Christoffersen, S.

Revision History (Full details and data files)

Version 1.0: 2015-04-29
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description

4ZFN | pdb_00004zfn

Hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRT) from Sulfolobus solfataricus containing GMP complexed in two different ways together with one or two MG2+

Literature

Sulfolobus solfataricus P2

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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