9NF6 | pdb_00009nf6

Cg10062 E114N mutant with a covalent hydroxypropionate and acrylate intermediate of the hydration of acetylenecarboxylic acid

PDB DOI: https://doi.org/10.2210/pdb9NF6/pdb

Classification: HYDROLASE
Organism(s): Corynebacterium glutamicum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-02-20 Released: 2025-04-02
Deposition Author(s): Silva, K., Geiger, J.H., Draths, K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free:
0.293 (Depositor), 0.291 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

Cg10062 E114N mutant with a covalent hydroxypropionate and acrylate intermediate of the hydration of acetylenecarboxylic acid

Silva, K., Geiger, J.H., Draths, K.

To be published.

Macromolecule Content

Total Structure Weight: 103.15 kDa
Atom Count: 7,294
Modeled Residue Count: 883
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-oxalocrotonate tautomerase	A, B, C, D, E A, B, C, D, E, F	148	Corynebacterium glutamicum	Mutation(s): 1 Gene Names: AUP69_07050, AUP70_06515
UniProt
Find proteins for A0A0S2T163 (Corynebacterium glutamicum) Explore A0A0S2T163 Go to UniProtKB: A0A0S2T163
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0S2T163
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth D] SDF format, chain K [auth E] SDF format, chain L [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth D] MOL2 format, chain K [auth E] MOL2 format, chain L [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth D] mmCIF format, chain K [auth E] mmCIF format, chain L [auth F]	G [auth A], J [auth D], K [auth E], L [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth D] Focus chain K [auth E] Focus chain L [auth F]
3OH Query on 3OH Download:Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	3-HYDROXY-PROPANOIC ACID C₃ H₆ O₃ ALRHLSYJTWAHJZ-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
AKR Query on AKR Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	ACRYLIC ACID C₃ H₄ O₂ NIXOWILDQLNWCW-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.63 Å
R-Value Free: 0.293 (Depositor), 0.291 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.396	α = 90
b = 88.062	β = 100.339
c = 79.318	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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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.