4MEJ | pdb_00004mej

Crystal structure of Lactobacillus helveticus purine deoxyribosyl transferase (PDT) with the tricyclic purine 8,9-dihydro-9-oxoimidazo[2,1-b]purine (N2,3-ethenoguanine)

PDB DOI: https://doi.org/10.2210/pdb4MEJ/pdb

Classification: transferase/transferase inhibitor
Organism(s): Lactobacillus helveticus H10
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-08-26 Released: 2014-10-15
Deposition Author(s): Paul, D., Seckute, J., Ealick, S.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.229 (Depositor), 0.229 (DCC)
R-Value Work:
0.195 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Glycosylation of a tricyclic purine analog at alternative sites by nucleoside 2 -deoxyribosyltransferases

Ye, W., Paul, D., Gao, L., Seckute, J., Sangaiah, R., Karupiah, J., Zhang, Z., Kaminski, A.P., Ealick, S.E., Gold, A., Ball, L.M.

(2014) PLoS One

Macromolecule Content

Total Structure Weight: 56.92 kDa
Atom Count: 4,292
Modeled Residue Count: 501
Deposited Residue Count: 501
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleoside deoxyribosyltransferase	A, B, C	167	Lactobacillus helveticus H10	Mutation(s): 0 Gene Names: LBHH_1694

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
28Y Query on 28Y Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth B]	3H-imidazo[2,1-b]purin-4(5H)-one C₇ H₅ N₅ O OSXKHFTZRHDUJN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain D [auth A]	D [auth A], H [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229 (Depositor), 0.229 (DCC)
R-Value Work: 0.195 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.695	α = 90
b = 79.695	β = 90
c = 186.697	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-10-15

Deposition Author(s):

Paul, D.

Seckute, J.

Ealick, S.E.

Revision History (Full details and data files)

Version 1.0: 2014-10-15
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Refinement description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description