3C87 | pdb_00003c87

Crystal structure of the enterobactin esterase FES from Shigella flexneri in the presence of enterobactin

PDB DOI: https://doi.org/10.2210/pdb3C87/pdb

Classification: HYDROLASE
Organism(s): Shigella flexneri 2a str. 2457T
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-02-11 Released: 2008-02-26
Deposition Author(s): Kim, Y., Maltseva, N., Abergel, R., Raymond, K., Holzle, D., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.190 (Depositor), 0.189 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3C87

This is version 1.2 of the entry. See complete history.

Literature

Siderophore Mediated Iron Acquisition: Structure and Specificity of Enterobactin Esterase from Shigella flexneri.

Kim, Y., Maltseva, N., Abergel, R., Raymond, K., Holzle, D., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 92.73 kDa
Atom Count: 6,697
Modeled Residue Count: 773
Deposited Residue Count: 806
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterochelin esterase	A, B	403	Shigella flexneri 2a str. 2457T	Mutation(s): 0 Gene Names: fes, S0503, SF0497 EC: 3.1.1.108
UniProt
Find proteins for A0A0H2VTI6 (Shigella flexneri) Explore A0A0H2VTI6 Go to UniProtKB: A0A0H2VTI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2VTI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-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, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.17 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.190 (Depositor), 0.189 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.305	α = 90
b = 113.245	β = 90
c = 151.123	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXL-97	phasing
RESOLVE	phasing
MLPHARE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-02-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-02-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-10-16
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.