3MFD

The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis

• PDB DOI: https://doi.org/10.2210/pdb3MFD/pdb

• Classification: HYDROLASE
• Organism(s): Bacillus subtilis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-01 Released: 2010-05-19 
• Deposition Author(s): Cuff, M.E., Rakowski, E., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

The Structure of the Beta-lactamase superfamily domain of D-alanyl-D-alanine carboxypeptidase from Bacillus subtilis.

Cuff, M.E., Rakowski, E., Buck, K., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 77.97 kDa 
• Atom Count: 6,071 
• Modelled Residue Count: 632 
• Deposited Residue Count: 668 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine carboxypeptidase dacB	A, B	334	Bacillus subtilis	Mutation(s): 0  Gene Names: BSU23190, dacB, DacC EC: 3.4.16.4
UniProt
Find proteins for P35150 (Bacillus subtilis (strain 168)) Explore P35150  Go to UniProtKB:  P35150

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	C [auth A], G [auth A], I [auth A], J [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	D [auth A], E [auth A], F [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.190 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.439	α = 90
b = 100.439	β = 90
c = 171.853	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Cuff, M.E., Rakowski, E., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary