6IGS | pdb_00006igs

Crystal structure of HPRT from F. tularensis with Zinc

PDB DOI: https://doi.org/10.2210/pdb6IGS/pdb

Classification: TRANSFERASE
Organism(s): Francisella tularensis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-25 Released: 2019-10-02
Deposition Author(s): Pavithra, G.C., Kundapura, S.V., Ramagopal, U.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.185 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of hypoxanthine phosphoribosyltransferase from Francisella tularensis

Pavithra, G.C., Ramagopal, U.A.

To be published.

Macromolecule Content

Total Structure Weight: 82.53 kDa
Atom Count: 5,512
Modeled Residue Count: 650
Deposited Residue Count: 708
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypoxanthine phosphoribosyltransferase	A, B, C, D	177	Francisella tularensis	Mutation(s): 0 Gene Names: hpt EC: 2.4.2.8
UniProt
Find proteins for Q5NI77 (Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4)) Explore Q5NI77 Go to UniProtKB: Q5NI77
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5NI77
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] I [auth B] L [auth C] M [auth C] E [auth A], F [auth A], I [auth B], L [auth C], M [auth C], P [auth D], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] J [auth B] K [auth B] N [auth C] G [auth A], H [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.16 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.185 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.764	α = 90
b = 90.193	β = 90
c = 113.707	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-10-02

Deposition Author(s):

Pavithra, G.C.

Kundapura, S.V.

Ramagopal, U.A.

Revision History (Full details and data files)

Version 1.0: 2019-10-02
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description