5EXG | pdb_00005exg

Crystal structure of recombinant dimeric Banana lectin

PDB DOI: https://doi.org/10.2210/pdb5EXG/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Musa acuminata
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-11-23 Released: 2016-12-07
Deposition Author(s): Struwe, W.B., Allison, T.A., Robinson, C.V., Benesch, J.L.P.B.
Funding Organization(s): Medical Research Council (United Kingdom), European Research Council, Biotechnology and Biological Sciences Research Council, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.198 (Depositor), 0.207 (DCC)
R-Value Work:
0.168 (Depositor), 0.181 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Glycan cluster recognition by a potent anti-HIV lectin exploiting bidentate binding amplified by tetrameric architecture

Hopper, J.T.S., Grant, O.C., Ambrose, S., Krumm, S., Allison, T.A., Pritchard, L.K., Tully, M., Ozorowsky, G., Ward, A.B., Crispin, M., Doores, K.J., Woods, R.J., Benesch, J.L.P.B., Robinson, C.V., Struwe, W.B.

To be published.

Macromolecule Content

Total Structure Weight: 31.99 kDa
Atom Count: 2,295
Modeled Residue Count: 282
Deposited Residue Count: 300
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ripening-associated protein	A, B	150	Musa acuminata	Mutation(s): 0
UniProt
Find proteins for O22321 (Musa acuminata) Explore O22321 Go to UniProtKB: O22321
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O22321
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.198 (Depositor), 0.207 (DCC)
R-Value Work: 0.168 (Depositor), 0.181 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.53	α = 90
b = 63.33	β = 90
c = 95.98	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-12-07

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	98101
European Research Council	United Kingdom	26851
Biotechnology and Biological Sciences Research Council	United Kingdom	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM094919
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103390
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1UM1AI100663

Revision History (Full details and data files)

Version 1.0: 2016-12-07
Type: Initial release
Version 1.1: 2017-08-30
Changes: Author supporting evidence
Version 1.2: 2021-07-21
Changes: Author supporting evidence
Version 1.3: 2022-03-30
Changes: Author supporting evidence, Database references
Version 1.4: 2024-01-10
Changes: Data collection, Refinement description