9FNK | pdb_00009fnk

The structure of CBM42 from Clostridium thermocellum

PDB DOI: https://doi.org/10.2210/pdb9FNK/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Acetivibrio thermocellus ATCC 27405
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-10 Released: 2025-06-25
Deposition Author(s): Hadad, N., Lavid, N., Shoham, Y., Shoham, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.287 (Depositor), 0.287 (DCC)
R-Value Work:
0.243 (Depositor), 0.243 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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This is version 1.0 of the entry. See complete history.

Literature

The structure of CBM42 from Clostridium thermocellum

Hadad, N., Lavid, N., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 98.01 kDa
Atom Count: 7,355
Modeled Residue Count: 800
Deposited Residue Count: 810
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anti-sigma-I factor RsgI5	A, B, C, D, E A, B, C, D, E, F	135	Acetivibrio thermocellus ATCC 27405	Mutation(s): 0 Gene Names: rsgI5, Cthe_1273
UniProt
Find proteins for A3DEX6 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)) Explore A3DEX6 Go to UniProtKB: A3DEX6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A3DEX6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth A] MOL2 format, chain N [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth A] mmCIF format, chain N [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth A]	H [auth A], I [auth C], J [auth C], K [auth D], N [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth D] Focus chain N [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth F] SDF format, chain O [auth F] SDF format, chain M [auth E] SDF format, chain L [auth E] MOL2 format, chain P [auth F] MOL2 format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth E] mmCIF format, chain P [auth F] mmCIF format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth E]	L [auth E], M [auth E], O [auth F], P [auth F]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain L [auth E] Focus chain M [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain L [auth E] Focus chain M [auth E] Focus chain O [auth F] Focus chain P [auth F]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.287 (Depositor), 0.287 (DCC)
R-Value Work: 0.243 (Depositor), 0.243 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.453	α = 92.639
b = 77.396	β = 110.062
c = 78.769	γ = 102.69

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
autoPROC	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-06-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-06-25
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.