4B52

Crystal structure of Gentlyase, the neutral metalloprotease of Paenibacillus polymyxa

Structural Biology Knowledgebase: 4B52 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4B52

Classification: HYDROLASE

Total Structure Weight: 66297.44

Macromolecule Entities
Molecule Chains Length Organism Details
BACILLOLYSIN A, B 304 Paenibacillus polymyxa EC#: 3.4.24.4 IUBMB
Fragment: RESIDUES 289-592
Mutation: S12T, I35V, A68T, R210T, N237T, L283Q
Gene Name(s): npr PPSC2_20195

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
RDF
Query on RDF

A, B N-ALPHA-L-RHAMNOPYRANOSYLOXY(HYDROXYPHOSPHINYL)- L-LEUCYL-L-TRYPTOPHAN
PHOSPHORAMIDON (Synonym)
C23 H34 N3 O10 P
ZPHBZEQOLSRPAK-XLCYBJAPSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000638 (TRP,LEU,RHA) A, B PHOSPHORAMIDON Glycopeptide /
Enzyme Inhibitor
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.247
  • R-Value Work: 0.195
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 61.12 α = 90.00
b = 77.02 β = 103.58
c = 64.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-02
  • Released Date: 2013-01-09
  • Deposition author(s): Ruf, A., Stihle, M., Benz, J., Schmidt, M., Sobek, H.

Revision History

  • 2013-07-24
    Type: Other | Details: Add PRD info
  • 2013-03-20
    Type: Atom nomenclature | Details: HETATM
  • 2013-03-06
    Type: Other | Details: Add PRD info
  • 2013-01-23
    Type: Citation | Details: JRNL