5TGF | pdb_00005tgf

Crystal structure of putative beta-lactamase from Bacteroides dorei DSM 17855

• PDB DOI: https://doi.org/10.2210/pdb5TGF/pdb

• Classification: HYDROLASE
• Organism(s): Phocaeicola dorei DSM 17855
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-09-27 Released: 2016-10-26 
• Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Literature

Crystal structure of a beta-lactamase from Bacteroides dorei DSM 17855

Nocek, B., Hatzos-Skintges, C., Joachimaik, A., Babnigg, G., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 150.51 kDa 
• Atom Count: 11,361 
• Modeled Residue Count: 1,331 
• Deposited Residue Count: 1,356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D	339	Phocaeicola dorei DSM 17855	Mutation(s): 0  Gene Names: BACDOR_00452
UniProt
Find proteins for B6VTD5 (Phocaeicola dorei DSM 17855) Explore B6VTD5  Go to UniProtKB:  B6VTD5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	E [auth A], F [auth A], G [auth B], H [auth C], I [auth C], K [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	J [auth C], L [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.475	α = 103.84
b = 68.292	β = 106.28
c = 88.216	γ = 101.2

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Nocek, B., Hatzos-Skintges, C., Babnigg, G., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary