7SF6 | pdb_00007sf6

Crystal Structure of Siderophore Binding Protein FatB from Desulfitobacterium hafniense

PDB DOI: https://doi.org/10.2210/pdb7SF6/pdb

Classification: METAL TRANSPORT
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-10-03 Released: 2021-12-15
Deposition Author(s): Kim, Y., Patel, H.P., Nordquist, K.A., Schaab, K.M., Sha, J., Babnigg, G., Bond, A.H., Joachimiak, A., Midwest Center for Structural Genomics, Midwest Center for Structural Genomics (MCSG)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.161 (Depositor), 0.162 (DCC)
R-Value Work:
0.137 (Depositor), 0.137 (DCC)
R-Value Observed:
0.138 (Depositor)

Starting Model: in silico
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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 Siderophore Binding Protein FatB from Desulfitobacterium hafniense

Kim, Y., Patel, H.P., Nordquist, K.A., Schaab, K.M., Sha, J., Babnigg, G., Bond, A.H., Joachimiak, A., Midwest Center for Structural Genomics

To be published.

Macromolecule Content

Total Structure Weight: 34.54 kDa
Atom Count: 2,904
Modeled Residue Count: 294
Deposited Residue Count: 314
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferric-anguibactin-binding protein FatB	A	314	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Dhaf_2916
UniProt
Find proteins for Q24WN9 (Desulfitobacterium hafniense (strain Y51)) Explore Q24WN9 Go to UniProtKB: Q24WN9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q24WN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DBS (Subject of Investigation/LOI) Query on DBS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID C₁₀ H₁₁ N O₆ VDTYHTVHFIIEIL-LURJTMIESA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]