3FXA

Crystal structure of a putative sugar-phosphate isomerase (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 A resolution

PDB DOI: https://doi.org/10.2210/pdb3FXA/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Listeria monocytogenes serotype 4b str. F2365
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-01-20 Released: 2009-02-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.157
R-Value Work: 0.133
R-Value Observed: 0.135

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of putative sugar-phosphate isomerase (YP_013136.1) from Listeria monocytogenes 4b F2365 at 1.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 86.64 kDa
Atom Count: 6,305
Modelled Residue Count: 766
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIS domain protein	A, B, C, D	201	Listeria monocytogenes serotype 4b str. F2365	Mutation(s): 0 Gene Names: LMOf2365_0531, YP_013136.1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth D] MOL2 format, chain E [auth B] MOL2 format, chain F [auth D] mmCIF format, chain E [auth B] mmCIF format, chain F [auth D]	E [auth B], F [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.157
R-Value Work: 0.133
R-Value Observed: 0.135
Space Group: P 3₁
Diffraction Data: https://doi.org/10.18430/M33FXA

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.944	α = 90
b = 57.944	β = 90
c = 197.964	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
PHASER	phasing
REFMAC	refinement
MolProbity	model building
PDB_EXTRACT	data extraction
MAR345	data collection
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-02-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-02-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations

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.