3FXA | pdb_00003fxa

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 (Depositor), 0.141 (DCC)
R-Value Work:
0.133 (Depositor), 0.141 (DCC)
R-Value Observed:
0.135 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3FXA

This is version 1.4 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
Modeled Residue Count: 766
Deposited Residue Count: 804
Unique protein chains: 1

Macromolecules

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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

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 F [auth D] SDF format, chain E [auth B] MOL2 format, chain F [auth D] MOL2 format, chain E [auth B] mmCIF format, chain F [auth D] mmCIF format, chain E [auth B]	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 (Depositor), 0.141 (DCC)
R-Value Work: 0.133 (Depositor), 0.141 (DCC)
R-Value Observed: 0.135 (Depositor)

Diffraction Data:

Space Group: P 3₁

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

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View more in-depth experimental data

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
Version 1.4: 2024-11-20
Changes: Data collection, Refinement description, 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.