4RXT | pdb_00004rxt

Crystal structure of carbohydrate transporter solute binding protein Arad_9553 from Agrobacterium Radiobacter, Target EFI-511541, in complex with D-arabinose

PDB DOI: https://doi.org/10.2210/pdb4RXT/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Rhizobium rhizogenes K84
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-11 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., Siedel, 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: 1.35 Å
R-Value Free:
0.205 (Depositor), 0.212 (DCC)
R-Value Work:
0.156 (Depositor), 0.168 (DCC)
R-Value Observed:
0.157 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Sugar Binding Transporter Arad_9553 from Agrobacterium Radiobacter, Target Efi-511541

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: 31.25 kDa
Atom Count: 2,515
Modeled Residue Count: 295
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter	A	299	Rhizobium rhizogenes K84	Mutation(s): 0 Gene Names: Arad_9553
UniProt
Find proteins for B9JKX8 (Rhizobium rhizogenes (strain K84 / ATCC BAA-868)) Explore B9JKX8 Go to UniProtKB: B9JKX8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9JKX8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARA Query on ARA Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	alpha-L-arabinopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-QMKXCQHVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.205 (Depositor), 0.212 (DCC)
R-Value Work: 0.156 (Depositor), 0.168 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.873	α = 90
b = 36.244	β = 110.01
c = 62.1	γ = 90

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

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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 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Structure summary