5ZC7 | pdb_00005zc7

Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 space group).

PDB DOI: https://doi.org/10.2210/pdb5ZC7/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pseudotuberculosis IP 32953
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-02-15 Released: 2019-02-20
Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.192 (Depositor), 0.196 (DCC)
R-Value Work:
0.160 (Depositor), 0.172 (DCC)
R-Value Observed:
0.162 (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 adenine phosphoribosyltransferase from Yersinia pseudotuberculosis

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

To be published.

Macromolecule Content

Total Structure Weight: 40.87 kDa
Atom Count: 2,943
Modeled Residue Count: 363
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine phosphoribosyltransferase	A, B	187	Yersinia pseudotuberculosis IP 32953	Mutation(s): 0 Gene Names: apt, YPTB0991 EC: 2.4.2.7
UniProt
Find proteins for Q66DQ2 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66DQ2 Go to UniProtKB: Q66DQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q66DQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE (Subject of Investigation/LOI) Query on ADE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B]	F [auth A], G [auth A], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	E [auth A], J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.192 (Depositor), 0.196 (DCC)
R-Value Work: 0.160 (Depositor), 0.172 (DCC)
R-Value Observed: 0.162 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.074	α = 90
b = 121.074	β = 90
c = 50.035	γ = 120

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-02-20

Deposition Author(s):

Pavithra, G.C.

Ramagopal, U.A.

Revision History (Full details and data files)

Version 1.0: 2019-02-20
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description

5ZC7 | pdb_00005zc7

Crystal structure of APRT from Y. pseudotuberculosis with bound adenine (P63 space group).

Literature

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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