2AC7

Crystal structure of Adenosine Phosphorylase from Bacillus cereus with adenosine bound in the active site

PDB DOI: https://doi.org/10.2210/pdb2AC7/pdb

Classification: TRANSFERASE
Organism(s): Bacillus cereus G9241
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-07-18 Released: 2006-07-18
Deposition Author(s): Rinaldo-Matthis, A., Allegrini, S., Sgarrella, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.202
R-Value Work: 0.177
R-Value Observed: 0.178

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Adenosine Phosphorylase from Bacillus cereus

Rinaldo-Matthis, A., Allegrini, S., Sgarrella, F.

To be published.

Macromolecule Content

Total Structure Weight: 52.13 kDa
Atom Count: 3,875
Modelled Residue Count: 441
Deposited Residue Count: 470
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	A, B	235	Bacillus cereus G9241	Mutation(s): 0 EC: 2.4.2.1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADN Query on ADN Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.202
R-Value Work: 0.177
R-Value Observed: 0.178
Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122	α = 90
b = 122	β = 90
c = 68	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
XDS	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-07-18

Deposition Author(s):

Rinaldo-Matthis, A.

Allegrini, S.

Sgarrella, F.

Revision History (Full details and data files)

Version 1.0: 2006-07-18
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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