7WEW | pdb_00007wew

Structure of adenylation domain of epsilon-poly-L-lysine synthase

PDB DOI: https://doi.org/10.2210/pdb7WEW/pdb

Classification: LIGASE
Organism(s): Streptomyces noursei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-12-24 Released: 2022-02-09
Deposition Author(s): Okamoto, T., Yamanaka, K., Hamano, Y., Nagano, S., Hino, T.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.220 (Depositor), 0.220 (DCC)
R-Value Work:
0.187 (Depositor), 0.186 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
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Literature

Crystal structure of the adenylation domain from an epsilon-poly-l-lysine synthetase provides molecular mechanism for substrate specificity

Okamoto, T., Yamanaka, K., Hamano, Y., Nagano, S., Hino, T.

(2022) Biochem Biophys Res Commun 596: 43-48

DOI: https://doi.org/10.1016/j.bbrc.2022.01.053

Macromolecule Content

Total Structure Weight: 55.05 kDa
Atom Count: 3,873
Modeled Residue Count: 481
Deposited Residue Count: 509
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epsilon-poly-L-lysine synthase	A	509	Streptomyces noursei	Mutation(s): 0 Gene Names: pls
UniProt
Find proteins for B5BR95 (Streptomyces noursei) Explore B5BR95 Go to UniProtKB: B5BR95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B5BR95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LAD (Subject of Investigation/LOI) Query on LAD Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	ADENOSINE-5'-[LYSYL-PHOSPHATE] C₁₆ H₂₆ N₇ O₈ P RZWIOOBQBMRZTQ-OPYVMVOTSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.220 (Depositor), 0.220 (DCC)
R-Value Work: 0.187 (Depositor), 0.186 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.511	α = 90
b = 152.511	β = 90
c = 48.202	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H02918
Japan Society for the Promotion of Science (JSPS)	Japan	16H06445
Japan Society for the Promotion of Science (JSPS)	Japan	19K06551