5Y4A

Cadmium directed assembly of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis.

PDB DOI: https://doi.org/10.2210/pdb5Y4A/pdb

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

Deposited: 2017-08-02 Released: 2018-08-08
Deposition Author(s): Pavithra, G.C., Ramagopal, U.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.255
R-Value Work: 0.198
R-Value Observed: 0.200

wwPDB Validation 3D Report Full Report

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

Literature

Cadmium directed assembly of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis.

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

To be published.

Macromolecule Content

Total Structure Weight: 41.23 kDa
Atom Count: 2,800
Modelled Residue Count: 359
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q66DQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	F [auth A], G [auth A], H [auth B], K [auth B], L [auth B]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B]	D [auth A], E [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain J [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.255
R-Value Work: 0.198
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.216	α = 90
b = 77.547	β = 90
c = 90.388	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Pavithra, G.C.

Ramagopal, U.A.

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2024-03-27
Changes: Data collection, Database references, Derived calculations, Refinement description