9QVL | pdb_00009qvl

Crystal structure of the CtaG_C11A variant from Ruminiclostridium cellulolyticum (P2(1)2(1)2(1)-small)

• PDB DOI: https://doi.org/10.2210/pdb9QVL/pdb

• Classification: LIGASE
• Organism(s): Ruminiclostridium cellulolyticum
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-04-11 Released: 2025-10-01 
• Deposition Author(s): Gude, F., Bohne, A., Dell, M., Franke, J., Dunbar, K.L., Groll, M., Hertweck, C.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.206 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

Literature

Distal peptide elongation by a protease-like ligase and two distinct carrier proteins

Gude, F., Bohne, A., Dell, M., Franke, J., Dunbar, K.L., Groll, M., Hertweck, C.

(2025) Chem : 102740

• DOI: https://doi.org/10.1016/j.chempr.2025.102740

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 37.47 kDa 
• Atom Count: 2,775 
• Modeled Residue Count: 312 
• Deposited Residue Count: 315 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Butirosin biosynthesis protein H N-terminal domain-containing protein	A	315	Ruminiclostridium cellulolyticum	Mutation(s): 1  Gene Names: Ccel_3254
UniProt
Find proteins for B8I0Y7 (Ruminiclostridium cellulolyticum (strain ATCC 35319 / DSM 5812 / JCM 6584 / H10)) Explore B8I0Y7  Go to UniProtKB:  B8I0Y7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
NI	B [auth A], C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.206 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.77	α = 90
b = 63.62	β = 90
c = 83.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-01 
Deposition Author(s): Gude, F., Bohne, A., Dell, M., Franke, J., Dunbar, K.L., Groll, M., Hertweck, C.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History  

• Version 1.0: 2025-10-01
  Type: Initial release