4IL2 | pdb_00004il2

Crystal structure of D-mannonate dehydratase (rspA) from E. coli CFT073 (EFI TARGET EFI-501585)

PDB DOI: https://doi.org/10.2210/pdb4IL2/pdb

Classification: LYASE
Organism(s): Escherichia coli CFT073
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-28 Released: 2013-02-20
Deposition Author(s): Lukk, T., Wichelecki, D., Imker, H.J., Gerlt, J.A., Nair, S.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.209 (Depositor), 0.206 (DCC)
R-Value Work:
0.178 (Depositor), 0.175 (DCC)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4IL2

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

Literature

Mannonate degradation pathway in E. coli CFT073

Wichelecki, S., Lukk, T., Imker, H.J., Nair, S.K., Gerlt, J.A.

To be published.

Macromolecule Content

Total Structure Weight: 195.78 kDa
Atom Count: 12,840
Modeled Residue Count: 1,545
Deposited Residue Count: 1,704
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Starvation sensing protein rspA	A, B, C, D	426	Escherichia coli CFT073	Mutation(s): 0 Gene Names: c1971, rspA EC: 4.2.1 (UniProt), 4.2.1.8 (UniProt)
UniProt
Find proteins for Q8FHC7 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore Q8FHC7 Go to UniProtKB: Q8FHC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8FHC7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.209 (Depositor), 0.206 (DCC)
R-Value Work: 0.178 (Depositor), 0.175 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.78	α = 90
b = 123.78	β = 90
c = 112.21	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2024-02-28
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.