4RJ2

Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution

PDB DOI: https://doi.org/10.2210/pdb4RJ2/pdb

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

Deposited: 2014-10-08 Released: 2014-12-03
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free: 0.189
R-Value Work: 0.176
R-Value Observed: 0.176

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution

Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

To be published.

Macromolecule Content

Total Structure Weight: 154.88 kDa
Atom Count: 12,253
Modelled Residue Count: 1,422
Deposited Residue Count: 1,422
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase DeoD-type	A, B, C, D, E A, B, C, D, E, F	237	Escherichia coli	Mutation(s): 0 Gene Names: deoD EC: 2.4.2.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth C] SDF format, chain I [auth D] SDF format, chain J [auth D] SDF format, chain K [auth D] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth C] MOL2 format, chain I [auth D] MOL2 format, chain J [auth D] MOL2 format, chain K [auth D] MOL2 format, chain L [auth F]	G [auth A] H [auth C] I [auth D] J [auth D] K [auth D] G [auth A], H [auth C], I [auth D], J [auth D], K [auth D], L [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth D] Focus chain K [auth D] Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.99 Å
R-Value Free: 0.189
R-Value Work: 0.176
R-Value Observed: 0.176
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.12	α = 90
b = 110.22	β = 111.08
c = 88.21	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-12-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-12-03
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Experimental preparation

Prepare Data

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Deposit Data

Help and Resources

4RJ2

Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution

Crystal structure of E.coli purine nucleoside phosphorylase at 0.99 A resolution

Entity ID: 1

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)