5DVY

2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium

• PDB DOI: https://doi.org/10.2210/pdb5DVY/pdb

• Classification: PENICILLIN-BINDING PROTEIN
• Organism(s): Enterococcus faecium DO
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-09-21 Released: 2015-10-07 
• Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Filippova, E., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.187 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Literature

2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.

Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Filippova, E., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 72.5 kDa 
• Atom Count: 5,254 
• Modelled Residue Count: 641 
• Deposited Residue Count: 647 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin binding protein 2 prime	A	647	Enterococcus faecium DO	Mutation(s): 0  Gene Names: pbp5, HMPREF0351_11456
UniProt
Find proteins for Q3XZN6 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)) Explore Q3XZN6  Go to UniProtKB:  Q3XZN6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.187 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 6₃ 2 2
• Diffraction Data: https://doi.org/10.18430/m35dvy

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.162	α = 90
b = 193.162	β = 90
c = 156.478	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
BLU-MAX	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Minasov, G., Wawrzak, Z., Shuvalova, L., Dubrovska, I., Flores, K., Filippova, E., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release