5HNM | pdb_00005hnm

Crystal structure of vancomycin resistance D,D-pentapeptidase VanY E175A mutant from VanB-type resistance cassette in complex with Zn(II)

• PDB DOI: https://doi.org/10.2210/pdb5HNM/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecalis V583
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-01-18 Released: 2016-02-10 
• Deposition Author(s): Stogios, P.J., Chun, J., Wawrzak, Z., Evdokimova, E., Di Leo, R., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

To be published

Stogios, P.J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

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

Biological assembly 5 assigned by authors.

Biological Assembly 6  

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

Biological assembly 6 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 135.09 kDa 
• Atom Count: 9,261 
• Modeled Residue Count: 1,077 
• Deposited Residue Count: 1,182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanyl-D-alanine carboxypeptidase	A, B, C, D, E, F	197	Enterococcus faecalis V583	Mutation(s): 1  Gene Names: vanYB, EF_2297 EC: 3.4.16.4 (PDB Primary Data), 3.4.17 (UniProt)
UniProt
Find proteins for Q47746 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q47746  Go to UniProtKB:  Q47746

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	H [auth A], J [auth B], N [auth E], P [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	G [auth A], I [auth B], K [auth C], L [auth D], M [auth E], O [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.275 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m35hnm

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.709	α = 101.34
b = 77.319	β = 108.13
c = 85.865	γ = 90.06

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-02-10 
Deposition Author(s): Stogios, P.J., Chun, J., Wawrzak, Z., Evdokimova, E., Di Leo, R., Yim, V., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2016-02-10
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description