7RU7 | pdb_00007ru7

Crystal structure of BtrK, a decarboxylase involved in butirosin biosynthesis

PDB DOI: https://doi.org/10.2210/pdb7RU7/pdb

Classification: LYASE
Organism(s): Niallia circulans
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-08-16 Released: 2022-08-17
Deposition Author(s): Arenas, L.A.R., Paiva, F.C.R., Huang, F., Leadlay, P., Dias, M.V.B.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.196 (Depositor), 0.198 (DCC)
R-Value Work:
0.177 (Depositor), 0.179 (DCC)
R-Value Observed:
0.178 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Crystal structure of BtrK, a decarboxylase involved in the (S)-4-amino-2-hydroxybutyrate (AHBA) formation during butirosin biosynthesis

Rivas Arenas, L.A., de Paiva, F.C., de O.Rossini, N., Li, Y., Spencer, J., Leadlay, P., Dias, M.V.

(2022) J Mol Struct 1267: 133576

DOI: https://doi.org/10.1016/j.molstruc.2022.133576

Macromolecule Content

Total Structure Weight: 50.4 kDa
Atom Count: 3,648
Modeled Residue Count: 412
Deposited Residue Count: 448
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-glutamyl-[BtrI acyl-carrier protein] decarboxylase	A	448	Niallia circulans	Mutation(s): 0 Gene Names: btrK EC: 4.1.1.95
UniProt
Find proteins for Q2L4H3 (Niallia circulans) Explore Q2L4H3 Go to UniProtKB: Q2L4H3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2L4H3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP (Subject of Investigation/LOI) Query on PLP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG (Subject of Investigation/LOI) Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.196 (Depositor), 0.198 (DCC)
R-Value Work: 0.177 (Depositor), 0.179 (DCC)
R-Value Observed: 0.178 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.912	α = 90
b = 129.544	β = 90
c = 45.721	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	18/00351-1

Revision History (Full details and data files)

Version 1.0: 2022-08-17
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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