4M3K | pdb_00004m3k

Structure of a single domain camelid antibody fragment cAb-H7S in complex with the BlaP beta-lactamase from Bacillus licheniformis

• PDB DOI: https://doi.org/10.2210/pdb4M3K/pdb

• Classification: HYDROLASE/IMMUNE SYSTEM
• Organism(s): Bacillus licheniformis, Lama glama
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-08-06 Released: 2014-08-06 
• Deposition Author(s): Pain, C., Kerff, F., Herman, R., Sauvage, E., Preumont, S., Charlier, P., Dumoulin, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Literature

Probing the mechanism of aggregation of polyQ model proteins with camelid heavy-chain antibody fragments

Pain, C., Cosolo, A., Preumont, S., Scarafone, N., Thorn, D., Herman, R., Spiegel, H., Pardon, E., Matagne, A., Charlier, P., Steyaert, J., Damblon, C., Kerff, F., Esposito, G., Dumoulin, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 44.01 kDa 
• Atom Count: 3,224 
• Modelled Residue Count: 376 
• Deposited Residue Count: 399 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	273	Bacillus licheniformis	Mutation(s): 0  Gene Names: penP, blaP EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808  Go to UniProtKB:  P00808

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Camelid heavy-chain antibody variable fragment cAb-H7S	B	126	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.818	α = 90
b = 42.94	β = 105.29
c = 74.818	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-06 
Deposition Author(s): Pain, C., Kerff, F., Herman, R., Sauvage, E., Preumont, S., Charlier, P., Dumoulin, M.

Revision History  

• Version 1.0: 2014-08-06
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary