4YLE | pdb_00004yle

Crystal structure of an ABC transpoter solute binding protein (IPR025997) from Burkholderia multivorans (Bmul_1631, Target EFI-511115) with an unknown ligand modelled as alpha-D-erythrofuranose

PDB DOI: https://doi.org/10.2210/pdb4YLE/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Burkholderia multivorans ATCC 17616
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-05 Released: 2015-04-15
Deposition Author(s): Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.211 (Depositor), 0.213 (DCC)
R-Value Work:
0.171 (Depositor), 0.174 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an ABC transporter solute binding protein (IPR025997) from Burkholderia multivorans (Bmul_1631, Target EFI-511115) with an unknown ligand modelled as alpha-D-erythrofuranose

Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Attonito, J.D., Scott Glenn, A., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 34.03 kDa
Atom Count: 2,353
Modeled Residue Count: 283
Deposited Residue Count: 316
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein/LacI transcriptional regulator	A	316	Burkholderia multivorans ATCC 17616	Mutation(s): 0 Gene Names: Bmul_1631, BMULJ_01611
UniProt
Find proteins for A0A0H3KJG7 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KJG7 Go to UniProtKB: A0A0H3KJG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H3KJG7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	B [auth A]	Unknown ligand		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.211 (Depositor), 0.213 (DCC)
R-Value Work: 0.171 (Depositor), 0.174 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.966	α = 90
b = 69.267	β = 90
c = 115.06	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-04-15

Deposition Author(s):

Enzyme Function Initiative (EFI)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM093342

Revision History (Full details and data files)

Version 1.0: 2015-04-15
Type: Initial release
Version 1.1: 2017-09-06
Changes: Author supporting evidence, Derived calculations, Source and taxonomy
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Structure summary