6SNU | pdb_00006snu

Crystal structure of the W60C mutant of the (S)-selective transaminase from Chromobacterium violaceum

PDB DOI: https://doi.org/10.2210/pdb6SNU/pdb

Classification: TRANSFERASE
Organism(s): Chromobacterium violaceum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2019-08-27 Released: 2019-10-09
Deposition Author(s): Ruggieri, F., Gustafsson, C., Kimbung, R.Y., Walse, B., Logan, D.T., Berglund, P.
Funding Organization(s): European Union

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.215 (Depositor), 0.222 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structures Combined with Molecular Dynamics Reveal Altered Flow of Water in the Active Site of W60C Chromobacterium violaceum omega-transaminase

Ruggieri, F., Gustafsson, C., Kimbung, R.Y., Walse, B., Logan, D.T., Berglund, P.

Not Published

Macromolecule Content

Total Structure Weight: 209.53 kDa
Atom Count: 14,564
Modeled Residue Count: 1,814
Deposited Residue Count: 1,860
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aspartate aminotransferase family protein	A, B, C, D	465	Chromobacterium violaceum	Mutation(s): 1 Gene Names: bioK, CBW21_20070, NCTC8684_01926 EC: 2.6.1
UniProt
Find proteins for A0A1R0MXM9 (Chromobacterium violaceum) Explore A0A1R0MXM9 Go to UniProtKB: A0A1R0MXM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1R0MXM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B], K [auth C], L [auth D]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B]