4ZJP | pdb_00004zjp

Structure of an ABC-Transporter Solute Binding Protein (SBP_IPR025997) from Actinobacillus Succinogenes (Asuc_0197, TARGET EFI-511067) with bound beta-D-ribopyranose

PDB DOI: https://doi.org/10.2210/pdb4ZJP/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Actinobacillus succinogenes 130Z
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-04-29 Released: 2015-05-20
Deposition Author(s): Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Glenn, A.S., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.185 (Depositor), 0.207 (DCC)
R-Value Work:
0.141 (Depositor)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure of an ABC-Transporter Solute Binding Protein (SBP_IPR025997) from Actinobacillus Succinogenes (Asuc_0197, TARGET EFI-511067) with bound beta-D-ribopyranose

Yadava, U., Vetting, M.W., Al Obaidi, N.F., Toro, R., Morisco, L.L., Benach, J., Wasserman, S.R., Attonito, J.D., Glenn, A.S., Chamala, S., Chowdhury, S., Lafleur, J., Love, J., Seidel, R.D., Whalen, K.L., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 31.04 kDa
Atom Count: 2,392
Modeled Residue Count: 270
Deposited Residue Count: 292
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Monosaccharide-transporting ATPase	A	292	Actinobacillus succinogenes 130Z	Mutation(s): 0 Gene Names: Asuc_0197 EC: 3.6.3.17
UniProt
Find proteins for A6VKT0 (Actinobacillus succinogenes (strain ATCC 55618 / DSM 22257 / CCUG 43843 / 130Z)) Explore A6VKT0 Go to UniProtKB: A6VKT0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6VKT0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIP Query on RIP 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]	beta-D-ribopyranose C₅ H₁₀ O₅ SRBFZHDQGSBBOR-TXICZTDVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [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: 1.63 Å
R-Value Free: 0.185 (Depositor), 0.207 (DCC)
R-Value Work: 0.141 (Depositor)
R-Value Observed: 0.144 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.261	α = 95.2
b = 37.416	β = 101.03
c = 48.165	γ = 97.09

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-05-20

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2015-05-20
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Refinement description, Source and taxonomy, Structure summary
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2023-11-15
Changes: Data collection
Version 1.4: 2024-11-20
Changes: Structure summary