4YO7

Crystal Structure of an ABC transporter solute binding protein (IPR025997) from Bacillus halodurans C-125 (BH2323, TARGET EFI-511484) with bound myo-inositol

PDB DOI: https://doi.org/10.2210/pdb4YO7/pdb

Classification: SOLUTE BINDING PROTEIN
Organism(s): Halalkalibacterium halodurans C-125
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-03-11 Released: 2015-03-25
Deposition Author(s): Yadava, U., 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.169
R-Value Work: 0.139
R-Value Observed: 0.140

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of an ABC transporter solute binding protein (IPR025997) from Bacillus halodurans C-125 (BH2323, TARGET EFI-511484) with bound myo-inositol

Yadava, U., 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)

To be published.

Macromolecule Content

Total Structure Weight: 35.96 kDa
Atom Count: 2,487
Modelled Residue Count: 287
Deposited Residue Count: 326
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar ABC transporter (Sugar-binding protein)	A	326	Halalkalibacterium halodurans C-125	Mutation(s): 0 Gene Names: BH2323
UniProt
Find proteins for Q9KAG4 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)) Explore Q9KAG4 Go to UniProtKB: Q9KAG4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9KAG4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
INS Query on INS Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C₆ H₁₂ O₆ CDAISMWEOUEBRE-GPIVLXJGSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [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: 0.169
R-Value Work: 0.139
R-Value Observed: 0.140
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.155	α = 90
b = 79.845	β = 90
c = 118.337	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-03-25

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2015-03-25
Type: Initial release
Version 1.1: 2024-10-16
Changes: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary

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4YO7

Crystal Structure of an ABC transporter solute binding protein (IPR025997) from Bacillus halodurans C-125 (BH2323, TARGET EFI-511484) with bound myo-inositol

Crystal Structure of an ABC transporter solute binding protein (IPR025997) from Bacillus halodurans C-125 (BH2323, TARGET EFI-511484) with bound myo-inositol

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)