4RY8

Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from Thermotoga lettingae TMO TARGET EFI-511109 in complex with 5-methylthioribose

PDB DOI: https://doi.org/10.2210/pdb4RY8/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Pseudothermotoga lettingae TMO
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-13 Released: 2014-12-24
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Al obaidi, N., Morisco, L.L., Wasserman, S.R., Chamala, S., Attonito, J.D., Scott glenn, A., Chowdhury, S., Lafleur, J., Hillerich, B., Siede, R.D., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.264
R-Value Work: 0.214
R-Value Observed: 0.216

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of 5-methylthioribose binding protein TLET_1677 from Thermotoga lettingae TARGET EFI-511109

Patskovsky, Y., Toro, R., Bhosle, R., Al obaidi, N., Chamala, S., Scott glenn, A., Attonito, J.D., Chowdhury, S., Lafleur, J., Siedel, R.D., Morisco, L.L., Wasserman, S.R., Hillerich, B., Love, J., Whalen, K.L., Gerlt, J.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 147.07 kDa
Atom Count: 10,412
Modelled Residue Count: 1,276
Deposited Residue Count: 1,316
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic binding protein	A, B, C, D	329	Pseudothermotoga lettingae TMO	Mutation(s): 0 Gene Names: Tlet_1677
UniProt
Find proteins for A8F7U7 (Pseudothermotoga lettingae (strain ATCC BAA-301 / DSM 14385 / NBRC 107922 / TMO)) Explore A8F7U7 Go to UniProtKB: A8F7U7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A8F7U7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SR1 Query on SR1 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C] mmCIF format, chain H [auth D]	E [auth A], F [auth B], G [auth C], H [auth D]	5-S-methyl-5-thio-alpha-D-ribofuranose C₆ H₁₂ O₄ S OLVVOVIFTBSBBH-KAZBKCHUSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.264
R-Value Work: 0.214
R-Value Observed: 0.216
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.622	α = 91.83
b = 67.848	β = 92.39
c = 83.653	γ = 89.93

Software Package:

Software Name	Purpose
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-12-24

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-12-24
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
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

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4RY8

Crystal structure of 5-methylthioribose transporter solute binding protein TLET_1677 from Thermotoga lettingae TMO TARGET EFI-511109 in complex with 5-methylthioribose

Crystal structure of 5-methylthioribose binding protein TLET_1677 from Thermotoga lettingae TARGET EFI-511109

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)