6DS2

Crystal structure of Ni(II)-bound human calprotectin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Biophysical Examination of the Calcium-Modulated Nickel-Binding Properties of Human Calprotectin Reveals Conformational Change in the EF-Hand Domains and His3Asp Site.

Nakashige, T.G.Bowman, S.E.J.Zygiel, E.M.Drennan, C.L.Nolan, E.M.

(2018) Biochemistry 57: 4155-4164


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A8
A, C, E, G
93Homo sapiensMutation(s): 1 
Gene Names: S100A8 (CAGA, CFAG, MRP8)
Find proteins for P05109 (Homo sapiens)
Go to Gene View: S100A8
Go to UniProtKB:  P05109
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A9
B, D, F, H
114Homo sapiensMutation(s): 0 
Gene Names: S100A9 (CAGB, CFAG, MRP14)
Find proteins for P06702 (Homo sapiens)
Go to Gene View: S100A9
Go to UniProtKB:  P06702
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C, D, E, F, G
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
B, C, D, E, F, H
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.145α = 90.00
b = 78.082β = 90.00
c = 223.787γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesCHE-1352132
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM126376
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM118695
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM069857

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references