7LM0 | pdb_00007lm0

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

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

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	D [auth A], E [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.196 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

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

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-09-22 
Deposition Author(s): Bury, P.S., Huang, F., Leadlay, P.F., Dias, M.V.B.

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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  

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