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

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:

(by identity cutoff) | 3D Structure

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% Identity50% Identity70% Identity90% Identity95% Identity100% 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

View Full Validation Report

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

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.