3TNY | pdb_00003tny

Structure of YfiY from Bacillus cereus bound to the siderophore iron (III) schizokinen

PDB DOI: https://doi.org/10.2210/pdb3TNY/pdb

Classification: METAL TRANSPORT
Organism(s): Bacillus cereus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-09-02 Released: 2012-09-05
Deposition Author(s): Clifton, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.189 (Depositor), 0.197 (DCC)
R-Value Work:
0.172 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands

Clifton, M.C., Rupert, P.B., Hoette, T.M., Raymond, K.N., Abergel, R.J., Strong, R.K.

To be published.

Macromolecule Content

Total Structure Weight: 34.93 kDa
Atom Count: 2,598
Modeled Residue Count: 280
Deposited Residue Count: 303
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YfiY (ABC transport system substrate-binding protein)	A	303	Bacillus cereus	Mutation(s): 0 Gene Names: yfiY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SKZ Query on SKZ 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]	[2-(hydroxy-kappaO)-4-[(3-{(hydroxy-kappaO)[1-(hydroxy-kappaO)ethenyl]amino}propyl)amino]-2-{2-[(3-{(hydroxy-kappaO)[1- (hydroxy-kappaO)ethenyl]amino}propyl)amino]-2-oxoethyl}-4-oxobutanoato(6-)-kappaO]iron C₁₆ H₂₂ Fe N₄ O₉ KGGQZTFRTARRPX-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.189 (Depositor), 0.197 (DCC)
R-Value Work: 0.172 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.796	α = 90
b = 47.328	β = 112.88
c = 64.981	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-09-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-05
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2019-02-27
Changes: Data collection, Database references
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.