5YH8

The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and nickel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanistic insights into staphylopine-mediated metal acquisition

Song, L.Zhang, Y.Chen, W.Gu, T.Zhang, S.Y.Ji, Q.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 3942-3947


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nickel ABC transporter substrate-binding protein
A
510Staphylococcus aureus (strain NCTC 8325)Mutation(s): 0 
Find proteins for Q2FVE7 (Staphylococcus aureus (strain NCTC 8325))
Go to UniProtKB:  Q2FVE7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
8UX
Query on 8UX

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Download CCD File 
A
(2~{S})-4-[[(2~{R})-3-(1~{H}-imidazol-4-yl)-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]-2-[[(2~{S})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]butanoic acid
staphylopine
C13 H20 N4 O6
WLNNYKMTYVPSDL-UJNFCWOMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.155 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 70.782α = 90.00
b = 85.474β = 90.00
c = 86.315γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
REFMACrefinement
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-09-27 
  • Released Date: 2018-03-28 
  • Deposition Author(s): Ji, Q., Song, L.

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references