4TN5 | pdb_00004tn5

Crystal Structure of Predicted Fructose Specific IIB from Escherichia Coli

PDB DOI: https://doi.org/10.2210/pdb4TN5/pdb
Entry: 4TN5 supersedes: 4JXD

Classification: TRANSFERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-03 Released: 2015-06-10
Deposition Author(s): Kim, M.S., Shin, D.H.
Funding Organization(s): NRF by MEST (NCRC), NRF by MEST (CRC), NRF by MEST

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free:
0.299 (Depositor), 0.306 (DCC)
R-Value Work:
0.223 (Depositor), 0.242 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4TN5

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

Literature

High-accuracy protein modeling and its application to molecular replacement of crystallographic phasing

Kim, M.S., Shin, D.H., Lee, J., Joo, K., Park, J., Lee, D., Berry, E.A., Jhon, G.-J.

To be published.

Macromolecule Content

Total Structure Weight: 25.64 kDa
Atom Count: 1,786
Modeled Residue Count: 226
Deposited Residue Count: 226
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-like phosphotransferase enzyme IIB component 3	A, B	113	Escherichia coli K-12	Mutation(s): 0 Gene Names: frwD, yijN, b3953, JW3925 EC: 2.7.1.69 (PDB Primary Data), 2.7.1.202 (UniProt)
UniProt
Find proteins for P32676 (Escherichia coli (strain K12)) Explore P32676 Go to UniProtKB: P32676
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32676
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI 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]	NICKEL (II) ION Ni VEQPNABPJHWNSG-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: 2.29 Å
R-Value Free: 0.299 (Depositor), 0.306 (DCC)
R-Value Work: 0.223 (Depositor), 0.242 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.11	α = 90
b = 33.11	β = 90
c = 154.281	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

This entry supersedes: 4JXD

Funding Organization	Location	Grant Number
NRF by MEST (NCRC)	Korea, Republic Of	2012-0000952
NRF by MEST (CRC)	Korea, Republic Of	2010K000266
NRF by MEST	Korea, Republic Of	2008-331-C0023
NRF by MEST	Korea, Republic Of	2010-0003907
NRF by MEST	Korea, Republic Of	2013R1A1A1A05008769

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, 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.