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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Ligand Structure Quality Assessment

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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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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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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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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.