7LLD | pdb_00007lld

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

PDB DOI: https://doi.org/10.2210/pdb7LLD/pdb

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

Deposited: 2021-02-03 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: 1.40 Å
R-Value Free:
0.188 (Depositor), 0.188 (DCC)
R-Value Work:
0.144 (Depositor), 0.144 (DCC)
R-Value Observed:
0.146 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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: 99.87 kDa
Atom Count: 8,479
Modeled Residue Count: 891
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-6' aminotransferase	A, B	446	Micromonospora echinospora	Mutation(s): 0 Gene Names: gntH, genB4, JD80_03664
UniProt
Find proteins for Q6QVT7 (Micromonospora echinospora) Explore Q6QVT7 Go to UniProtKB: Q6QVT7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6QVT7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SBV (Subject of Investigation/LOI) Query on SBV Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-beta-L-threo-hexopyranoside C₂₇ H₄₉ N₆ O₁₂ P RIDGEVUBNCTQEZ-LVJYRULHSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
YS7 (Subject of Investigation/LOI) Query on YS7 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,3,4,6-tetradeoxy-6-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]-alpha-D-erythro-hexopyranoside C₂₇ H₄₉ N₆ O₁₂ P RIDGEVUBNCTQEZ-IXQBVWJDSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
PG4 Query on PG4 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]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], H [auth B], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.188 (Depositor), 0.188 (DCC)
R-Value Work: 0.144 (Depositor), 0.144 (DCC)
R-Value Observed: 0.146 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.455	α = 90
b = 75.036	β = 90
c = 186.031	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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