9QVS | pdb_00009qvs

Crystal structure of the CtaG_D144N variant from Ruminiclostridium cellulolyticum (P2(1)-small)

PDB DOI: https://doi.org/10.2210/pdb9QVS/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.182 (Depositor), 0.185 (DCC)
R-Value Work:
0.156 (Depositor), 0.156 (DCC)
R-Value Observed:
0.157 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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

Macromolecule Content

Total Structure Weight: 37.21 kDa
Atom Count: 2,695
Modeled Residue Count: 308
Deposited Residue Count: 315
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8I0Y7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.182 (Depositor), 0.185 (DCC)
R-Value Work: 0.156 (Depositor), 0.156 (DCC)
R-Value Observed: 0.157 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.61	α = 90
b = 60.28	β = 108.76
c = 54.84	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XFIT	data reduction
pointless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-01

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-01
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.