9K0B | pdb_00009k0b

Structure of Pictet-Spenglerases KslB in complex with L-Trp

PDB DOI: https://doi.org/10.2210/pdb9K0B/pdb

Classification: LIGASE
Organism(s): Kitasatospora
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-10-15 Released: 2025-06-18
Deposition Author(s): Mori, T., Renata, H., Abe, I.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.250 (Depositor), 0.249 (DCC)
R-Value Work:
0.207 (Depositor), 0.206 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structure of Pictet-Spenglerases KslB

Mori, T., Renata, H., Abe, I.

To be published.

Macromolecule Content

Total Structure Weight: 75.11 kDa
Atom Count: 4,928
Modeled Residue Count: 576
Deposited Residue Count: 674
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cucumopine synthase C-terminal helical bundle domain-containing protein	A, B	337	Kitasatospora	Mutation(s): 0 Gene Names: KSE_70640
UniProt
Find proteins for E4NIM4 (Kitasatospora setae (strain ATCC 33774 / DSM 43861 / JCM 3304 / KCC A-0304 / NBRC 14216 / KM-6054)) Explore E4NIM4 Go to UniProtKB: E4NIM4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E4NIM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRP (Subject of Investigation/LOI) Query on TRP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-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: 2.10 Å
R-Value Free: 0.250 (Depositor), 0.249 (DCC)
R-Value Work: 0.207 (Depositor), 0.206 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.768	α = 90
b = 82.102	β = 90
c = 91.704	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-06-18

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-06-18
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.