5IBQ | pdb_00005ibq

Crystal structure of an ABC solute binding protein from Rhizobium etli CFN 42 (RHE_PF00037,TARGET EFI-511357) in complex with alpha-D-apiose

PDB DOI: https://doi.org/10.2210/pdb5IBQ/pdb

Classification: SOLUTE-BINDING PROTEIN
Organism(s): Rhizobium etli CFN 42
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-02-22 Released: 2016-04-20
Deposition Author(s): Vetting, M.W., Carter, M.S., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free:
0.164 (Depositor), 0.164 (DCC)
R-Value Work:
0.150 (Depositor), 0.151 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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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 an ABC solute binding protein from Rhizobium etli CFN 42 (RHE_PF00037,TARGET EFI-511357) in complex with alpha-D-apiose

Vetting, M.W., Carter, M.S., Al Obaidi, N.F., Morisco, L.L., Benach, J., Koss, J., Wasserman, S.R., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 33.29 kDa
Atom Count: 2,630
Modeled Residue Count: 287
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ribose ABC transporter, substrate-binding protein	A	310	Rhizobium etli CFN 42	Mutation(s): 0 Gene Names: RHE_PF00037
UniProt
Find proteins for Q2JZQ5 (Rhizobium etli (strain ATCC 51251 / DSM 11541 / JCM 21823 / NBRC 15573 / CFN 42)) Explore Q2JZQ5 Go to UniProtKB: Q2JZQ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2JZQ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XXM Query on XXM 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]	3-C-(hydroxylmethyl)-alpha-D-erythrofuranose C₅ H₁₀ O₅ ASNHGEVAWNWCRQ-VAYJURFESA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.20 Å
R-Value Free: 0.164 (Depositor), 0.164 (DCC)
R-Value Work: 0.150 (Depositor), 0.151 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.272	α = 90
b = 36.924	β = 118.02
c = 95.619	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-04-20

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2016-04-20
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary