4PIW | pdb_00004piw

Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12

PDB DOI: https://doi.org/10.2210/pdb4PIW/pdb

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

Deposited: 2014-05-09 Released: 2014-07-16
Deposition Author(s): Wang, F., Xu, W., Helmich, K.E., Singh, S., Yennamalli, R.M., Miller, M.D., Bingman, C.A., Thorson, J.S., Phillips Jr., G.N., Enzyme Discovery for Natural Product Biosynthesis (NatPro)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.275 (Depositor), 0.272 (DCC)
R-Value Work:
0.236 (Depositor), 0.237 (DCC)
R-Value Observed:
0.237 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.3 of the entry. See complete history.

Literature

Crystal structure of sugar aminotransferase WecE from Escherichia coli K-12

Wang, F., Xu, W., Helmich, K.E., Singh, S., Yennamalli, R.M., Bingman, C.A., Miller, M.D., Thorson, J.S., Phillips Jr., G.N.

To be published.

Macromolecule Content

Total Structure Weight: 359.64 kDa
Atom Count: 22,917
Modeled Residue Count: 2,888
Deposited Residue Count: 3,168
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TDP-4-keto-6-deoxy-D-glucose transaminase family protein	A, B, C, D, E A, B, C, D, E, F, G, H	396	Escherichia coli K-12	Mutation(s): 0 Gene Names: wecE EC: 2.6.1.59
UniProt
Find proteins for P27833 (Escherichia coli (strain K12)) Explore P27833 Go to UniProtKB: P27833
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27833
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP Query on LLP	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₁₄ H₂₂ N₃ O₇ P		LYS
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.275 (Depositor), 0.272 (DCC)
R-Value Work: 0.236 (Depositor), 0.237 (DCC)
R-Value Observed: 0.237 (Depositor)

Diffraction Data:

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.341	α = 90
b = 87.483	β = 91.1
c = 161.554	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHENIX	phasing
PDB_EXTRACT	data extraction
PHENIX	refinement
XSCALE	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2014-07-16

Deposition Author(s):

Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U01GM098248

Revision History (Full details and data files)

Version 1.0: 2014-07-16
Type: Initial release
Version 1.1: 2015-10-14
Changes: Data collection
Version 2.0: 2017-09-27
Changes: Author supporting evidence, Derived calculations, Non-polymer description, Refinement description, Structure summary
Version 2.1: 2019-12-25
Changes: Author supporting evidence
Version 2.2: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 2.3: 2023-11-15
Changes: Data collection