7LLE | pdb_00007lle

Crystal structure of GenB4 in complex with PLP

PDB DOI: https://doi.org/10.2210/pdb7LLE/pdb

Classification: TRANSFERASE
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: 1.70 Å
R-Value Free:
0.184 (Depositor), 0.187 (DCC)
R-Value Work:
0.154 (Depositor), 0.155 (DCC)
R-Value Observed:
0.154 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.0 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: 98.66 kDa
Atom Count: 8,197
Modeled Residue Count: 891
Deposited Residue Count: 892
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.184 (Depositor), 0.187 (DCC)
R-Value Work: 0.154 (Depositor), 0.155 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71	α = 90
b = 74.21	β = 90
c = 181	γ = 90

Software Package:

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

Structure Validation

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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

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release

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