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)

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35150
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B]	C [auth A], G [auth A], I [auth A], J [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B]	D [auth A] E [auth A] F [auth A] H [auth A] K [auth B] 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		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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