5HCH | pdb_00005hch

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair

PDB DOI: https://doi.org/10.2210/pdb5HCH/pdb
NAKB: 5HCH

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-04 Released: 2016-03-02
Deposition Author(s): Roethlisberger, P., Istrate, A., Marcaida Lopez, M.J., Visini, R., Stocker, A., Leumann, C.J.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.257 (Depositor), 0.230 (DCC)
R-Value Work:
0.227 (Depositor), 0.210 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

X-ray structure of a lectin-bound DNA duplex containing an unnatural phenanthrenyl pair.

Roethlisberger, P., Istrate, A., Marcaida Lopez, M.J., Visini, R., Stocker, A., Reymond, J.L., Leumann, C.J.

(2016) Chem Commun (Camb) 52: 4749-4752

PubMed: 26898721 Search on PubMed
DOI: https://doi.org/10.1039/c6cc00374e
Primary Citation of Related Structures:
5HCH

PubMed Abstract:
DNA duplexes containing unnatural base-pair surrogates are attractive biomolecular nanomaterials with potentially beneficial photophysical or electronic properties. Herein we report the first X-ray structure of a duplex containing a phen-pair in the center of the double helix in a zipper like stacking arrangement.

Organizational Affiliation

Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland. christian.leumann@dcb.unibe.ch.

Macromolecule Content

Total Structure Weight: 20.1 kDa
Atom Count: 1,409
Modelled Residue Count: 140
Deposited Residue Count: 140
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucose-binding lectin	A	114	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020... lecB, AN280_27645, AN399_05715, AN400_17270, AN446_25935, AN447_15925, AOD73_08535, AOX61_23230, AOX62_26425, APG03_22020, APG04_23970, APG05_03535, APG06_28020, APG07_27985, ERS445055_01627, PA8380_17510, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713, PAO1OR1608
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5 Go to UniProtKB: Q9HYN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HYN5
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(CPGPCPAPTPTP(DF)PTPAPTPCPGP*C)-3')	B	13	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PGPCPGPAPTPAP(DF)PAPAPTPGPCP*G)-3')	C [auth E]	13	synthetic construct
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
61J Query on 61J Download Ideal Coordinates CCD File SDF format, chain G [auth E] MOL2 format, chain G [auth E] mmCIF format, chain G [auth E]	G [auth E]	(6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol C₈ H₁₇ O₇ P VFSMFEFBFABRKT-TVNFTVLESA-N		Interactions Focus chain G [auth E] Interactions & Density Focus chain G [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.257 (Depositor), 0.230 (DCC)
R-Value Work: 0.227 (Depositor), 0.210 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.451	α = 90
b = 60.451	β = 90
c = 204.828	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-03-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	20020_146646

Revision History (Full details and data files)

Version 1.0: 2016-03-02
Type: Initial release
Version 1.1: 2016-03-30
Changes: Database references
Version 1.2: 2017-09-13
Changes: Author supporting evidence, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description