3MWF | pdb_00003mwf

Crystal structure of Staphylococcus aureus SirA complexed with staphyloferrin B

PDB DOI: https://doi.org/10.2210/pdb3MWF/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Staphylococcus aureus subsp. aureus N315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-05-05 Released: 2010-09-01
Deposition Author(s): Grigg, J.C., Murphy, M.E.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.206 (Depositor), 0.205 (DCC)
R-Value Work:
0.182 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Staphylococcus aureus SirA specificity for staphyloferrin B is driven by localized conformational change

Grigg, J.C., Cheung, J., Heinrichs, D.E., Murphy, M.E.

To be published.

Macromolecule Content

Total Structure Weight: 33.84 kDa
Atom Count: 2,589
Modeled Residue Count: 292
Deposited Residue Count: 298
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-regulated ABC transporter siderophore-binding protein SirA	A	298	Staphylococcus aureus subsp. aureus N315	Mutation(s): 0 Gene Names: SA0111, sirA

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SE8 Query on SE8 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]	5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoic acid C₁₆ H₂₄ N₄ O₁₁ SIAZVTIHOHTZDD-PWJLMRLQSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
FE Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.206 (Depositor), 0.205 (DCC)
R-Value Work: 0.182 (Depositor), 0.182 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.719	α = 90
b = 71.588	β = 90
c = 72.568	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-09-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-09-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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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.