7QXF | pdb_00007qxf

Fructose-6-phosphate aldolase (FSA) mutant R134V, S166G, with covalently bound active site ligand

PDB DOI: https://doi.org/10.2210/pdb7QXF/pdb

Classification: LYASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2022-01-26 Released: 2023-02-08
Deposition Author(s): Dobritzsch, D., Widersten, M., Engel, S.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.262 (Depositor), 0.237 (DCC)
R-Value Work:
0.220 (Depositor)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history.

Literature

Engineered aldolases catalyzing stereoselective aldol reactions between aryl-substituted ketones and aldehydes

Cornelius, E.C., Bartl, M., Persson, L.J., Xiong, R., Cederfelt, D., Rad, F.M., Norberg, T., Engel, S., Marklund, E.G., Dobritzsch, D., Widersten, M.

(2023) Catal Sci Technol 13: 4978-4987

DOI: https://doi.org/10.1039/D3CY00181D

Macromolecule Content

Total Structure Weight: 359.08 kDa
Atom Count: 24,511
Modeled Residue Count: 3,307
Deposited Residue Count: 3,405
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-6-phosphate aldolase 1	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	227	Escherichia coli	Mutation(s): 2 Gene Names: fsaA, fsa, mipB, ybiZ, b0825, JW5109 EC: 4.1.2
UniProt
Find proteins for P78055 (Escherichia coli (strain K12)) Explore P78055 Go to UniProtKB: P78055
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78055
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
I2F Query on I2F	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	L-PEPTIDE LINKING	C₁₂ H₂₆ N₂ O₅		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.262 (Depositor), 0.237 (DCC)
R-Value Work: 0.220 (Depositor)
R-Value Observed: 0.222 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.198	α = 90
b = 176.865	β = 91.5
c = 120.093	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-02-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private		194-0638
Other private		183-358
Other private	Sweden	2019-01-24

Revision History (Full details and data files)

Version 1.0: 2023-02-08
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection, Derived calculations
Version 1.3: 2024-02-07
Changes: Refinement description
Version 1.4: 2024-10-16
Changes: 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.