4WVI

Crystal structure of the Type-I signal peptidase from Staphylococcus aureus (SpsB) in complex with a substrate peptide (pep2).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Peptide binding to a bacterial signal peptidase visualized by peptide tethering and carrier-driven crystallization.

Ting, Y.T.Harris, P.W.Batot, G.Brimble, M.A.Baker, E.N.Young, P.G.

(2016) IUCrJ 3: 10-19


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,Signal peptidase IB
A
533Escherichia coli O157:H7Staphylococcus aureus (strain COL)
This entity is chimeric
Mutation(s): 2 
Gene Names: malE, spsB
EC: 3.4.21.89
Find proteins for P0AEY0 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AEY0
Find proteins for Q5HHB9 (Staphylococcus aureus (strain COL))
Go to UniProtKB:  Q5HHB9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
substrate peptide (pep2)
D
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.989α = 90.00
b = 80.232β = 90.00
c = 119.879γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Aimlessdata scaling
XDSdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Health Research CouncilNew Zealand--

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2016-02-17
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Data collection, Derived calculations, Refinement description
  • Version 1.3: 2018-04-25
    Type: Data collection, Database references
  • Version 1.4: 2018-06-13
    Type: Data collection