6FFL

Maltose/maltodextrin-binding domain MalE from Bdellovibrio bacteriovorus bound to maltotriose

PDB DOI: https://doi.org/10.2210/pdb6FFL/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bdellovibrio bacteriovorus HD100
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-01-08 Released: 2018-01-24
Deposition Author(s): Licht, A., Werther, T., Bommer, M., Neumann, K., Schneider, E.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.191
R-Value Work: 0.158
R-Value Observed: 0.160

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 44.96 kDa
Atom Count: 3,554
Modelled Residue Count: 383
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose/maltodextrin transport permease homologue	A	388	Bdellovibrio bacteriovorus HD100	Mutation(s): 0 Gene Names: malF, Bd1227
UniProt
Find proteins for Q6MNM0 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MNM0 Go to UniProtKB: Q6MNM0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6MNM0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B	3		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G96370VA GlyCosmos: G96370VA GlyGen: G96370VA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-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] 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]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900009 Query on PRD_900009	B	alpha-maltotriose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.191
R-Value Work: 0.158
R-Value Observed: 0.160
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.747	α = 90
b = 106.692	β = 90
c = 53.492	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
AutoSol	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-01-24

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB1078

Revision History (Full details and data files)

Version 1.0: 2018-01-24
Type: Initial release
Version 1.1: 2018-01-31
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2018-10-10
Changes: Data collection, Database references
Version 1.3: 2019-02-20
Changes: Data collection, Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

6FFL

Maltose/maltodextrin-binding domain MalE from Bdellovibrio bacteriovorus bound to maltotriose

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)