4RK9 | pdb_00004rk9

CRYSTAL STRUCTURE OF SUGAR TRANSPORTER BL01359 FROM Bacillus licheniformis, TARGET EFI-510856, IN COMPLEX WITH STACHYOSE

PDB DOI: https://doi.org/10.2210/pdb4RK9/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Bacillus licheniformis DSM 13 = ATCC 14580
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-10-12 Released: 2014-11-05
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Attonito, J.D., Scott Glenn, A., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.272 (Depositor), 0.275 (DCC)
R-Value Work:
0.194 (Depositor), 0.202 (DCC)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

CRYSTAL STRUCTURE OF SUGAR TRANSPORTER BL01359 FROM Bacillus licheniformis, TARGET EFI-510856

Patskovsky, Y., Toro, R., Bhosle, R., Al Obaidi, N., Chamala, S., Scott Glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 92.32 kDa
Atom Count: 6,432
Modeled Residue Count: 768
Deposited Residue Count: 802
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbohydrate ABC transporter substrate-binding protein MsmE	A, B	401	Bacillus licheniformis DSM 13 = ATCC 14580	Mutation(s): 0 Gene Names: msmE, BL01359, BLi01140
UniProt
Find proteins for Q65LL6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65LL6 Go to UniProtKB: Q65LL6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q65LL6
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-galactopyranose-(1-6)-[beta-D-fructofuranose-(2-1)]alpha-D-glucopyranose	C, D	4		N/A	Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G21073BE GlyCosmos: G21073BE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.272 (Depositor), 0.275 (DCC)
R-Value Work: 0.194 (Depositor), 0.202 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.332	α = 90
b = 85.916	β = 90
c = 132.58	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-05

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-11-05
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-02-28
Changes: Data collection, Database references, Structure summary