5G5Z

S.pneumoniae ABC-transporter substrate binding protein FusA in complex with kestose

PDB DOI: https://doi.org/10.2210/pdb5G5Z/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Streptococcus pneumoniae TIGR4
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-10 Released: 2017-01-18
Deposition Author(s): Culurgioni, S., Harris, G., Singh, A.K., King, S.J., Walsh, M.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.222
R-Value Work: 0.168
R-Value Observed: 0.171

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 227.33 kDa
Atom Count: 17,104
Modelled Residue Count: 1,964
Deposited Residue Count: 1,972
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC TRANSPORTER, SUBSTRATE-BINDING PROTEIN	A, B, C, D	493	Streptococcus pneumoniae TIGR4	Mutation(s): 0
UniProt
Find proteins for A0A0H2URD6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2URD6 Go to UniProtKB: A0A0H2URD6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0H2URD6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	E, F, G, H	3		N/A	Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H
Glycosylation Resources
GlyTouCan: G11260CN GlyCosmos: G11260CN

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain J [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain O [auth D] SDF format, chain Q [auth D] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth D]	I [auth A] J [auth A] K [auth B] L [auth B] M [auth C] I [auth A], J [auth A], K [auth B], L [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900029 Query on PRD_900029	E, F, G, H	1-kestose	Oligosaccharide / Nutrient		Interactions Focus chain E Focus chain F Focus chain G Focus chain H Interactions & Density Focus chain E Focus chain F Focus chain G Focus chain H

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.222
R-Value Work: 0.168
R-Value Observed: 0.171
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.61	α = 90
b = 127.82	β = 96.58
c = 120.55	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

5G5Z

S.pneumoniae ABC-transporter substrate binding protein FusA in complex with kestose

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)