7LM0

Crystal structure of GenB3 in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb7LM0/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Micromonospora echinospora
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-02-04 Released: 2021-09-22
Deposition Author(s): Bury, P.S., Huang, F., Leadlay, P.F., Dias, M.V.B.
Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.196
R-Value Work: 0.161
R-Value Observed: 0.163

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of GenB4 in complex with external aldimine of PLP-sisomicin

Bury, P.S., Huang, F., Leadlay, P.F., Dias, M.V.B.

(2021) ACS Catal

Macromolecule Content

Total Structure Weight: 98.87 kDa
Atom Count: 7,583
Modelled Residue Count: 895
Deposited Residue Count: 898
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-6' aminotransferase	A, B	449	Micromonospora echinospora	Mutation(s): 0 Gene Names: gacC, gntJ, genB3
UniProt
Find proteins for Q2MG50 (Micromonospora echinospora) Explore Q2MG50 Go to UniProtKB: Q2MG50
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2MG50
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 D [auth A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B]	D [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 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: 2.09 Å
R-Value Free: 0.196
R-Value Work: 0.161
R-Value Observed: 0.163
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.531	α = 90
b = 156.753	β = 115.2
c = 63.893	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2014/15971-3
Sao Paulo Research Foundation (FAPESP)	Brazil	2015/09188-8
Sao Paulo Research Foundation (FAPESP)	Brazil	2018/00351-1

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description

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7LM0

Crystal structure of GenB3 in complex with PLP

Crystal structure of GenB4 in complex with external aldimine of PLP-sisomicin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)